Author Archives: TinaS

August 2, 2018

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In today’s Microbiome Digest you can read about: the connection of mother’s microbiota and development of psychiatric disorders by M.G. Codagnone; pulmonary microbiome by A.N. Costa; microbiome and allergic diseases by M.Pascal; olfactory communication via microbiota in birds by O. Maraci; global topsoil microbiome by M. Bahram and many more. Enjoy your hot summer read!

Pregnancy and early life

Review: Programming Bugs: Microbiota and the Developmental Origins of Brain Health and Disease – Martin G.Codagnone – Biological Psychiatry

Human respiratory microbiome

The pulmonary microbiome: challenges of a new paradigm – André Nathan Costa – Jornal Brasileiro de Pneumologia

Oral microbiology

Are the mutans streptococci still considered relevant to understanding the microbial etiology of dental caries? – Jeffrey A. Banas – BMC Oral Health

Predicting oral malodour based on the microbiota in saliva samples using a deep learning approach – Yoshio Nakano – BMC Oral Health

Human skin microbiome

The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome – Kang Kang – Cell Reports

Human gut microbiome

Alterations in the Gut Microbiota of Rats Chronically Exposed to Volatilized Cocaine and Its Active Adulterants Caffeine and Phenacetin – Cecilia Scorza – Neurotoxicity Research

Origination, change, and modulation of geriatric disease-related gut microbiota during life – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens – Alexandra E. Livanos – PLOS One

Minireview: Microbiome and Allergic Diseases – Mariona Pascal – Frontiers in Immunology / Mucosal Immunity

Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy – Xingming Deng – Frontiers in Microbiology / Antimicrobials, Resistance and Chemotherapy

Moxibustion treatment modulates the gut microbiota and immune function in a dextran sulphate sodium-induced colitis rat model – Qin Qi – World Journal of Gastroenterology

Helicobacter pylori in human health and disease: Mechanisms for local gastric and systemic effects – Denisse Bravo – World Journal of Gastroenterology

Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species – Valentina Laclare McEneany – The ISME Journal

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance – Aspen T. Reese – mBio

Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs – Celeste Alexander – British Journal of Nutrition

Standardization of gut microbiota analysis: Variability in samples taken at different times from single case and the effect of the freezing the sample – F. Saglam – International Journal of Infectious Diseases

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size – Emily C. Hoedt – The ISME journal

Animal experiments 

A Polysaccharide Isolated from Dictyophora indusiata Promotes Recovery from Antibiotic-Driven Intestinal Dysbiosis and Improves Gut Epithelial Barrier Function in a Mouse Model – Sadia Kanwal – Nutrients

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis – Simon Ghaly – Scientific Reports

Treatment with camu camu (Myrciaria dubia) prevents obesity by altering the gut microbiota and increasing energy expenditure in diet-induced obese mice – Fernando F Anhê – Gut Microbiota

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures – Matej Medvecky – BMC Genomics

Addition of arabinoxylan and mixed linkage glucans in porcine diets affects the large intestinal bacterial populations – John B. Gorham – European Journal of Nutrition

Animal microbiome 

A prokaryotic-eukaryotic relation in the fat body of Bombus terrestris – Anneleen Parmentier – Environmental Microbiology Reports

Olfactory Communication via Microbiota: What Is Known in Birds? – Öncü Maraci – Genes

Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta) – Alexandria Creasy – Viruses

Plant, root, and soil microbiome

Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field – Pranitha S. Pandit – Antonie van Leeuwenhoek

Long-term effects of untreated wastewater on soil bacterial communities – Tianlin Shen – Science of The Total Environment

Minireview: Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation – Sara Correa-García – Microbial Biotechnology

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana Fusarium wilt disease by reshaping the soil microbiome – Zongzhuan Shen – Biology and Fertility of Soils

Structure and function of the global topsoil microbiome – Mohammad Bahram – Nature

Globally rising soil heterotrophic respiration over recent decades – Ben Bond-Lamberty – Nature

Water and extremophile microbiome

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current – Flavia Flaviani – Frontiers in Microbiology / Aquatic Microbiology

Evaluation of biomethane potential of waste algal biomass collected from eutrophied lake: effect of source of inocula, co-substrate, and VS loading – Pushpendar Kumar – Journal of Applied Phycology

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria – Xiufeng Ma – Environmental Microbiology

Increased biofilm formation due to high-temperature adaptation in marine Roseobacter – Alyssa G. Kent – Nature Microbiology

Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms – Frank Unfried – The ISME Journal

The anchoring effect—long-term dormancy and genetic population structure – Lisa Sundqvist – The ISME Journal

Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments – Stefan Spring – Environmental Microbiology

The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients – Julia M. Otte – Environmental Microbiology

Temporal and spatial dynamics in microbial community composition within a temperate stream network – Norman Hassell – Environmental Microbiology

Diel dynamics and coupling of heterotrophic prokaryotes and dissolved organic matter in epipelagic and mesopelagic waters of the central Red Sea – Francisca C. García – Environmental Microbiology

Probiotics / prebiotics

The effects of a multispecies probiotic on migraine and markers of intestinal permeability–results of a randomized placebo-controlled study – N M de Roos – European Journal of Clinical Nutrition

Phages and viruses

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis – Tanmoy Chakraborty – Virulence

Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race – Amelia McKitterick – bioRxiv

Bioinformatics

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea – Johannes Alneberg – Scientific Data

Bacteria & Art

The Beautiful World of Bacteria

 

July 03, 2018

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In today’s Digest you can read about: soil microbes regulating forest succession by H. Liao,  sinking particles in the ocean microbiome by M. Mestre, ecology and evolution of seafloor and subseafloor microbial communities by W. D. Orsi, biotechnological potentials of marine bacteria by A. K.  Farha, differentiation of Candida species Raman spectroscopy by A. Silge. Enjoy your summer read!

General microbiome

Signatures of ecological processes in microbial community time series – Karoline Faust – Microbiome

Review: Metabolic reprogramming for cancer cells and their microenvironment: Beyond the Warburg Effect – Linchong Sun – Biochimica et Biophysica Acta (BBA) – Reviews on Cancer

Oral microbiota

Microbial similarity and preference for specific sites in healthy oral cavity and esophagus – Li Dong – Frontiers in Microbiology / Microbial Symbioses

Human gut microbiome

Altered Gut Microbiota: A Link Between Diet and the Metabolic Syndrome – Velasquez Manuel T. – Metabolic Syndrome and Related Disorders

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut – Whitman B. Schofield – Cell Host & Microbe

Plant, root, and soil microbiome

Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession – Patrick J. Kearns – The ISME Journal

Links among warming, carbon and microbial dynamics mediated by soil mineral weathering – S. Doetterl – Nature Geoscience

In Planta Bacterial Transcriptomics Predict Plant Disease Outcomes – Stephen P.Cohen – Trends in Plant Science

Hymenobacter jeollabukensis sp. nov., isolated from soil – Leonid N. Ten -Journal of Microbiology

Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant Kandelia candel – Lv Zhang –  International Journal of Systematic and Evolutionary Microbiology

Soil microbes regulate forest succession in a subtropical ecosystem in China: evidence from a mesocosm experiment – Huixuan Liao – Plant and Soil

Solubilization of insoluble zinc compounds by zinc solubilizing bacteria (ZSB) and optimization of their growth conditions – Mohammad Yaghoubi Khanghahi – Environmental Science and Pollution Research

Soil microbial communities differ according to fertiliser regimes and cabbage (Brassica oleracea var. capitata L.) growth, but not aphid herbivory – Flora J. O’Brien – Frontiers in Microbiology / Terrestrial Microbiology

Paenibacillus elymi sp. nov., isolated from the rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea – Ye-Ji Hwang – International Journal of Systematic and Evolutionary Microbiology

Changes in rhizosphere microbial communities in potted cucumber seedlings treated with syringic acid – Zhilin Wang – PLOS One

Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays – Sarah A. Maarastawi – Frontiers in Microbiology / Terrestrial Microbiology

Isolation of Pseudomonas putida from Harir/Erbil soil and screening for the presence of phosphate solubilizing genes – Aras Mohammed Khudhur – Polytechnic Journal

Environmental controls on soil microbial communities in a seasonally dry tropical forest – Silvia Pajaresa – Applied and Environmental Microbiology

Temperature effects on structure and function of the methanogenic microbial communities in two paddy soils and one desert soil – Pengfei Liu – Soil Biology and Biochemistry

Soil microbial communities differ according to fertiliser regimes and cabbage (Brassica oleracea var. capitata L.) growth, but not aphid herbivory – Flora J. O’Brien – Frontiers in Microbiology

Natural forests maintain a greater soil microbial diversity than that in rubber plantations in Southwest China –  Jutamart Monkai – Agriculture, Ecosystems & Environment

Water and extremophile microbiome 

Sinking particles promote vertical connectivity in the ocean microbiome – Mireia Mestre – PNAS

Filtering artefacts in bacterial community composition can affect the outcome of dissolved organic matter biolability assays – Joshua F. Dean – Biogeosciences

Review: Ecology and evolution of seafloor and subseafloor microbial communities – William D. Orsi  – Nature Reviews Microbiology

The unexpected diversity of microbial communities associated with black corals revealed by high-throughput Illumina sequencing – Yong-Chun Liu  – FEMS Microbiology Letters

Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates – Lloyd D Potts – FEMS Microbiology Ecology

Microbial distribution and turnover in Antarctic microbial mats highlight the relevance of heterotrophic bacteria in low-nutrient environments – Patricia M Valdespino-Castillo – FEMS Microbiology Ecology

Cultivation and characterization of Candidatus Nitrosotenuis aquariensis, an ammonia-oxidizing archaeon from a freshwater aquarium biofilter – Laura A. Sauder – Applied and Environmental Microbiology

Biofilm and planktonic bacterial communities in a drinking water distribution system supplied with untreated groundwater – Jianfei Chen – Archives of Microbiology

Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil  – Hernando P. Bacosa – The ISME Journal

A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales – Connor B.Driscoll – Harmful Algae

Review: Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production – Sheeja Jagadevan – Biotechnology for Biofuels

Phylogenetic diversity and biotechnological potentials of marine bacteria from continental slope of eastern Arabian Sea – Arakkaveettil Kabeer Farha – Journal of Genetic Engineering and Biotechnology

Biochemical methane potential of microalgae biomass using different microbial inocula – Cristina Gonzalez-Fernandez – Biotechnology for Biofuels

Quorum sensing in thermophiles: prevalence of autoinducer-2 system – Amandeep Kaur – BMC Microbiology

Molecular Cloning and Characterization of a Novel α-Amylase from Antarctic Sea Ice Bacterium Pseudoalteromonas sp. M175 and Its Primary Application in Detergent – Xiaofei Wang – BioMed Research International

Low-temperature sulfidic-ice microbial communities, Borup Fiord Pass, Canadian high Arctic – Christopher B. Trivedi – Frontiers in Microbiology / Extreme Microbiology

Phages and viruses

Beyond members of the Flaviviridae family, sofosbuvir also inhibits chikungunya virus replication – Andre Ferreira – bioRxiv

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses – Marcos Parras-Moltó – Microbiome

Immuno-metabolic changes in herpes virus infection – Debprasa Chattopadhyay – Cytokine

Emergence of a Virulent Genotype VIIi of Newcastle Disease Virus in Iran – Arash Ghalyanchilangeroudi – Avian Pathology

Techniques

High-throughput microfluidic sorting of live magnetotactic bacteria – Andy Tay – Applied and Environmental Microbiology

The application of UV resonance Raman spectroscopy for the differentiation of clinically relevant Candida species – Anja Silge – Analytical and Bioanalytical Chemistry

June 27, 2018

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In today’s Microbiome Digest you can read about: cyanobacterial blooms by J. Huisman, designer microbial consortia by W. Kong,  the significance of the intestinal microbiome for vaccinology by Vanessa C. Harris, indigenous microbes residing in oil sands by Xiaoxuan Yu, effects of sliver nanoparticles on soil microbiome by J.Y. Xu,  WHAM!: a web-based visualization tool for metagenomics by J.C. Devlin. Yet another interesting read you can find in Science & Publishing  –> “Death of scientific journals after 350 years” by S. Silver. Enjoy!

General microbiome

Designing microbial consortia with defined social interactions –  Wentao Kong – Nature Chemical Biology

Pregnancy and early life

Antibiotics in early life: dysbiosis and the damage done – Hadar Neuman – FEMS Microbiology Reviews

Human ear microbiota

The unsolved problem of otitis media in indigenous populations: A systematic review of upper respiratory and middle ear microbiota in indigenous children – Andrea Coleman – bioRxiv

Human respiratory microbiome

Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human gut microbiome

Alterations in the gut bacterial microbiome in fungal Keratitis patients – Sama Kalyana Chakravarthy – PLOS One

Altered intestinal microbiota composition, antibiotic therapy and intestinal inflammation in children and adolescents with cystic fibrosis – Maiara Brusco de Freitas – PLOS One

Nonaplex PCR using Cliffhanger primers to identify diarrhoeagenic Escherichia coli from crude lysates of human faecal samples – Uffe Vest Schneider – PLOS One

Review: The Significance of the Intestinal Microbiome for Vaccinology: From Correlations to Therapeutic Applications – Vanessa C. Harris – Drugs

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics – Emiro Buendía – Scientific Reports

Role of Microbiota and Tryptophan Metabolites in the Remote Effect of Intestinal Inflammation on Brain and Depression – Barbora Waclawiková – Pharmaceuticals

The study of bacteria in biopsies from Slovak colorectal adenoma and carcinoma patients – L. Wachsmannova-  Neoplasma

Amplification of Antimicrobial Resistance in Gut Flora of Patients Treated with Ceftriaxone – J. Meletiadis – Antimicrobial Agents and Chemotherapy

Animal experiments 

Metabolome disruption of pregnant rats and their offspring resulting from repeated exposure to a pesticide mixture representative of environmental contamination in Brittany – Nathalie Bonvallot – PLOS One

Dietary supplementation with raspberry extracts modifies the fecal microbiotain obese diabetic db/db mice –    Jose F. Garcia-Mazcorro – Journal of Microbiology and Biotechnology

Effects of dietary yeast nucleotides supplementation on intestinal barrier function, intestinal microbiota, and humoral immunity in specific pathogen-free chickens – Che Wu – Poultry Science

Magnesium lithospermate B improves the gut microbiome and bile acid metabolic profiles in a mouse model of diabetic nephropathy – Jing Zhao – Acta Pharmacologica Sinica

Animal microbiome

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs – Rebecca Flancman – PLOS One

Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island – Takashi Hayakawa – Primates

Plant, root, and soil microbiome

Indigenous microorganisms residing in oil sands tailings biodegrade residual bitumen – Xiaoxuan Yu – Chemosphere

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars – Shobit Thapa – Archives of Microbiology

Large-scale replicated field study of maize rhizosphere identifies heritable microbes – William A. Walters – PNAS

Long-term effects of sliver nanoparticles on the abundance and activity of soil microbiome – Jing Yang Xu – Journal of Environmental Sciences

Long-term effects of environmentally relevant concentrations of silver nanoparticles on microbial biomass, enzyme activity, and functional genes involved in the nitrogen cycle of loamy soil – Anna-Lena Grün – Journal of Environmental Sciences

Sphingomonas tabacisoli sp. nov., a member of the genus Sphingomonas, isolated from rhizosphere soil of Nicotiana tabacum L. – Xing-Kui Zhou – International Journal of Systematic and Evolutionary Microbiology

Effects of Bacillus subtilis and nanohydroxyapatite on the metal accumulation and microbial diversity of rapeseed (Brassica campestris L.) for the remediation of cadmium-contaminated soil – Wei Liu – Environmental Science and Pollution Research

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars – Shobit Thapa – Archives of Microbiology

Water and extremophile microbiome

Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity – Jose Flores-Uribe – bioRxiv

Comparative genomics analyses indicate differential methylated amine utilisation trait within the member of the genus Gemmobacter – Eileen Kröber – bioRxiv

Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance – Wana Lailan Oliveira da Costa – PLOS One

Factors affecting infection of corals and larval oysters by Vibrio coralliilyticus – Blake Ushijima – PLOS One

“Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘omics” –  Xyrus X Maurer-Alcalá – Genome Biology and Evolution

Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride – Xikun Liu – FEMS Microbiology Ecology

Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation – Jian Guo –  Nature Microbiology

Warming and oligotrophication cause shifts in freshwater phytoplankton communities – Laura Verbeek – Global Change Biology

Review: Cyanobacterial blooms – Jef Huisman – Nature Reviews Microbiology

Research letter: Airborne Microbes Contribute to N2 Fixation in Surface Water of the Northern Red Sea – Eyal Rahav – Geophysical Research Letters

Bloom of a denitrifying methanotroph, “Candidatus Methylomirabilis limnetica”, in a deep stratified lake – Jon S. Graf – Environmental Microbiology

Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea – Elisabeth Happel – Environmental Microbiology

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice‐covered lakes – Patricia Tran – Environmental Microbiology

Rapid thermal adaptation in a marine diatom reveals constraints and tradeoffs – Daniel R. O’Donnell – Global Change Biology

A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses – Qiang Zheng – Frontiers in Microbiology / Virology

Built environment 

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales – Mikayla A. Borton – PNAS

Phages and viruses

Two point mutations in the Hantaan virus glycoproteins afford the generation of a highly infectious recombinant vesicular stomatitis virus vector – Megan M Slough – bioRxiv

ΦCrAss001, a member of the most abundant bacteriophage family in the human gut, infects Bacteroides – Andrey Shkoporov – bioRxiv

In silico characterisation of the two-component system regulators of Streptococcus pyogenes – Sean J. Buckley- PLOS One

Host-microbiome interactions

Opinion: Classic Models for New Perspectives: Delving into Helminth–Microbiota–Immune System Interactions – Alba Cortés – Trends in Parasitology

Review: Helminth–Bacterial Interactions: Cause and Consequence – Alexis Rapin – Trends in Immunology

Bioinformatics

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data – Joseph C. Devlin – BMC Genomics

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples – Ehsaneddin Asgari – Bioinformatics

Science, publishing, and career 

The Impact of Grant Funding on the Publication Activity of Awarded Applicants: A Systematic Review of Comparative Studies and Meta-analytical Estimates – Ruslan Saygitov – bioRxiv

Death of scientific journals after 350 years – Simon Silver – FEMS Microbiology Letters

June 19, 2018

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In today’s digest you can read about: the field of CRISPR-CAS antimicrobials by E. Pursey, “microbiota influencers” by G. Rizzatti, bioplastic producing bacterial communities by V. Kumar, mixotrophic behavior of the harmful benthic dinoflagellate by B. Lee and many many diverse and interesting articles. Enjoy!

General microbiome

CRISPR-Cas antimicrobials: Challenges and future prospects – Elizabeth Pursey – PLOS Pathogens

Considering Microbial CO2 during Microbe-Plant Cocultivation – Birgit Piechulla – Plant Physiology

Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss – Colin P. McNally  – BMC Systems Biology

Pregnancy and early life

Prevalence of antibiotic resistance in commensal Escherichia coli among the children in rural hill communities of Northeast India – Ashish Kumar Singh – PLOS One

Shared and Distinct Features of Human Milk and Infant Stool Viromes – Pia S. Pannaraj – Frontiers in Microbiology

Preterm infant gut microbial patterns related to the development of necrotizing enterocolitis – Tristan P. Lindberg – The Journal of Maternal-Fetal & Neonatal Medicine

Human respiratory microbiome

Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4 – Irene Jiménez-Munguía – PeerJ

Human gut microbiome

Addendum: “I will survive”: A tale of bacteriophage-bacteria coevolution in the gut – Luisa De Sordi – Gut Microbes

The Gut-Associated Microbiome of the Eastern Spruce Budworm Does Not Influence Larval Growth or Survival – Melbert T Schwarz – bioRxiv

Prioritizing and modelling of putative drug target proteins of Candida albicans by systems biology approach – Tariq Ismail – Acta Biochimica Polonica

Antibiotic and Modulation of Microbiota: A New Paradigm? – Gianenrico Rizzatti – Journal of Clinical Gastroenterology

Streptomyces, shared microbiome member of soil and gut, as “old friends” against colon cancer – Alireza Bolourian – FEMS Microbiology Ecology

Gut Microbial-related Choline Metabolite Trimethylamine-N-oxide is Associated with Progression of Carotid Artery Atherosclerosis in HIV Infection – Zhilei Shan – The Journal of Infectious Diseases

Role of Microbiota in Sexually Dimorphic Immunity – Marlies Elderman – Frontiers in Immunology

Early results of fecal microbial transplantation protocol implementation at a community-based university hospital – Rodrigo Duarte-Chavez – Journal of Global Infectious Diseases

Gut microbiota modulate neurobehavior through changes in brain insulin sensitivity and metabolism – Marion Soto – Molecular Psychiatry

The Rise and Rise of Eosinophilic Gut Diseases Including Eosinophilic Esophagitis Is Probably Not Explained by the Disappearance of Helicobacter pylori, so Who or What’s to Blame? – Nicholas J. Talley – The American Journal of Gastroenterology

Effect of administration of a probiotic preparation on gut microbiota and immune response in healthy women in India: an open-label, single-arm pilot study – Ankita Singh – BMC Gastroenterology

Animal experiments

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile – Lucie Etienne-Mesmin – Gut microbiome

Animal microbiome

A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach – Sarayu Bhogoju – PLOS One

Tracking sources of Clostridium botulinum type E contamination in seal meat – Daniel Leclair – International Journal of Circumpolar Health

Plant, root, and soil microbiome

Applying predictive models to decipher rhizobacterial modifications in common reed die-back affected populations – Giovanni Bacci – Science of The Total Environment

Bioplastic reservoir of diverse bacterial communities revealed along altitude gradient of Pangi-Chamba trans-Himalayan region – Vijay Kumar – FEMS Microbiology Letters

Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp – Valentina Maggini – FEMS Microbiology Ecology

Divergent Responses of the Diazotrophic Microbiome to Elevated CO2 in Two Rice Cultivars – Yongjie Yu – Frontiers in Microbiology

Synthesis and detoxification of nitric oxide in the plant beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 and its effect on biofilm formation – Xiaoyan Dong – Biochemical and Biophysical Research Communications

Understanding the Strategies to Overcome Phosphorus–Deficiency and Aluminum–Toxicity by Ryegrass Endophytic and Rhizosphere Phosphobacteria – Patricio J. Barra – Frontiers in Microbiology

Soil viruses are underexplored players in ecosystem carbon processing – Gareth Trubl – bioRxiv

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities –  Eric M Bottos – FEMS Microbiology Ecology

Changes of soil microbial and enzyme activities are linked to soil C, N and P stoichiometry in afforested ecosystems – F.Z. Zhao – Forest Ecology and Management

Responses of soil microbial communities to nutrient limitation in the desert-grassland ecological transition zone – Cui Y – The Science of the Total Environment

Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange – Dušan Veličković – The ISME Journal

Antibacterial activity of soil bacteria isolated from Kochi, India and their molecular identification – Davis Gislin – Journal of Genetic Engineering and Biotechnology

Brassica napus Growth in Lead-Polluted Soil: Bioaccumulation in Plant Organs at Different Ontogenetic Stages and Lead Fractionation in Soil – Gisele V. Ferreyroa – Water, Air, & Soil Pollution

Editorial: “Plant-Microbe-Insect Interaction: Source for Bio-fertilizers, Bio-medicines and Agent Research” – Gero Benckiser – Frontiers in Plant Science

Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere – Fernando Uriel Rojas-Rojas – Microbiology

Improvement of Ni phytoextraction by Alyssum murale and its rhizosphere microbial activities by applying nitrogen fertilizer – Ali Kanso – Ecological Research

Water and extremophile microbiome

Abundance determines the functional role of bacterial phylotypes in complex communities – Damian W. Rivett  – Nature Microbiology

Metabolic Diversity within the Globally Abundant Marine Group II Euryarchaea Drives Ecological Patterns – Benjamin J Tully – bioRxiv

Diversity of bacterial communities and dissolved organic matter in a temperate estuary – Helena Osterholz – FEMS Microbiology Ecology

Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms – Zhi-Ping Zhong – Frontiers in Microbiology

Genetic diversity and co-occurrence patterns of marine cyanopodoviruses and picocyanobacteria – Yingting Sun – Applied and Environmental Microbiology

Proteome response of a metabolically flexible anoxygenic phototroph to Fe(II) oxidation – Casey Bryce – Applied and Environmental Microbiology

Genome rearrangement shapes Prochlorococcus ecological adaptation – Wei Yan – Applied and Environmental Microbiology

High CO2 Under Nutrient Fertilization Increases Primary Production and Biomass in Subtropical Phytoplankton Communities: A Mesocosm Approach – Nauzet Hernández-Hernández – Frontiers in Microbiology

Genetic Analyses of the rbcL and psaA Genes From Single Cells Demonstrate a Rhodophyte Origin of the Prey in the Toxic Benthic Dinoflagellate Ostreopsis – Bora Lee – Frontiers in Marine Science

Ubiquitous abundance distribution of non-dominant plankton across the global ocean – Enrico Ser-Giacomi – Nature Ecology & Evolution

Copiotrophic marine bacteria are associated with strong iron‐binding ligand production during phytoplankton blooms – Shane L. Hogle – Limnology and Oceanography

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling – David M. Needham – The ISME Journal

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom – Yuanyuan Xue – The ISME Journal

Coral Microbiomes as Bioindicators of Reef Health – Sofia Roitman – Population Genomics

Microbial community structure and functional potential along a hypersaline gradient – Jeffrey A. Kimbrel – Frontiers in Microbiology

Comparative genomics of Pseudomonas sp. strain SI-3 associated with macroalga Ulva prolifera, the causative species for green tide in the Yellow Sea – Huihui Fu – Frontiers in Microbiology

Probiotics / prebiotics

Pilot assessment of probiotics for pregnant women in Rwanda – Amy McMillan – PLOS One

Phages and viruses

Low spatial structure and selection against secreted virulence factors attenuates pathogenicity in Pseudomonas aeruginosa – Elisa T Granato – bioRxiv

Identification of anti-norovirus genes in mouse and human cells using genome-wide CRISPR activation screening –  Robert Orchard – bioRxiv

Biotechnology

Simultaneous autotrophic removal of sulphate and nitrate at different voltages in a bioelectrochemical reactor (BER): Evaluation of degradation efficiency and characterization of microbial communities – Hao Xua – Bioresource Technology

Evaluation of A Novel Split-Feeding Anaerobic/Oxic Baffled Reactor (A/OBR) For Foodwaste Anaerobic Digestate: Performance, Modeling and Bacterial Community – Shaojie Wang – Scientific Reports

Viewpoint: Synthetic Biology for Natural Compounds – Xinrui Zhao – Biochemistry

Bioinformatics

iMetaLab 1.0: A web platform for metaproteomics data analysis – Bo Liao – Bioinformatics

Taxonomy annotation and guide tree errors in 16S rRNA databases – Robert Edgar​ – PeerJ

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level – Luis M Rodriguez-R – Nucleic Acids Research

Techniques

Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates – Michal Strejcek – Frontiers in Microbiology

Low-power portable devices for metagenomics analysis: Fog computing makes bioinformatics ready for the Internet of Things –  Ivan Merelli – Future Generation Computer Systems

Microbes in the news 

Unique microbe could thrive on Mars, help future manned missions

In a Warming World, Deadly Bacteria Are More Resistant to Antibiotics

Microbes on the market

Startup aims to make allies of human gut’s microbes

Department of Energy Announces $40 Million for Bio-Based Research

Tina’s non-microbiology picks

Towards an Evolutionary Perspective in Teaching and Popularizing Microbiology – Fernando Bueno Ferreira Fonseca de Fraga – Journal of  Microbiology & Biology Education

 

May 29, 2018

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Today we have an interesting review discussing the best practices for performing a microbiome study by R. Knight, “Microbial wars” – a brief overview on microbial competition by M.A. Bauer. Check many other interesting papers, particularly “crowded” section of Soil microbes, while in news you can read how scientists tested bacteria’s power to boost broccoli growth in space. Enjoy!

General microbiome

Review: Best practices for analysing microbiomes – Rob Knight – Nature Reviews Microbiology

Microbial wars: Competition in ecological niches and within the microbiome – Maria A. Bauer – Microbial Cell

Review: Concepts and Methods to Access Novel Antibiotics from Actinomycetes – Joachim J. Hug  – Antibiotics

 

 

Human gut microbiome

Gut Microbiota and Human Health: Insights From Ecological Restoration – Matthew R. Orr – The Quarterly Review of Biology

Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota – Ruairi C. Robertson – Microbiome

Current Evidence for the Management of Inflammatory Bowel Diseases Using Fecal Microbiota Transplantation – Seong Ran Jeon – Current Infectious Disease Reports

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species – Melhem Bilen – Microbiome

Animal experiments

Gut microbes contribute to variation in solid organ transplant outcomes in mice – Christine M. McIntosh – Microbiome

Animal microbiome 

Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota – Fanshu Xiao – Current Microbiology

Microbial shifts in the swine nasal microbiota in response to parenteral antimicrobial administration – Mohamed Zeineldin – Microbial Pathogenesis

Photobacterium malacitanum sp. nov., and Photobacterium andalusiense sp. nov., two new bacteria isolated from diseased farmed fish in Southern Spain – Alejandro M. Labella – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Effects of genetically modified Burkholderia pyrrocinia JK-SH007E1 on soil microbial community in poplar rhizosphere – L. He – Forest Pathology

Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China – Dong Liu – PLOS One

Short-term transcriptional response of microbial communities to N-fertilization in a pine forest soil – Michaeline B.N. Albright – Applied and Environmental Microbiology

Spatial structuring of soil microbial communities in commercial apple orchards – Greg Deakin – Applied Soil Ecology

Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China – Dong Liu – PLOS One

Effects of winter snowpack and nitrogen addition on the soil microbial community in a temperate forest in northeastern China – Guoyong Yan – Ecological Indicators

Responses of soil bacterial communities to Conyza canadensis invasion with different cover classes along a climatic gradient* – Congyan Wang – CLEAN Soil Water

Shifts in microbial community structure and soil nitrogen mineralization following short-term soil amendment with the ammonifier Bacillus amyloliquefaciens DT – Cai Hui – International Biodeterioration & Biodegradation

Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China – Xiaoyan Sun – Environmental Science and Pollution Research

Enhancer assisted-phytoremediation of mercury-contaminated soils by Oxalis corniculata L., and rhizosphere microorganism distribution of Oxalis corniculata L. – Zhongchuang Liu – Ecotoxicology and Environmental Safety

Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4, Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata – Abanoub E. Wanees – Genome Announcements

Cultivar-specific response of bacterial community to cadmium contamination in the rhizosphere of rice (Oryza sativa L.)  – Dandi Hou – Environmental Pollution

Elevated CO2 increases the abundance but simplifies networks of soybean rhizosphere fungal community in Mollisol soils – Zhenhua Yu – Agriculture, Ecosystems & Environment

Suppression of Alternaria blight disease and plant growth promotion of mustard (Brassica juncea L.) by antagonistic rhizosphere bacteria – R. Sharma – Applied Soil Ecology

Water and extremophile microbiome

Salipaludibacillus halalkaliphilus sp. nov., a moderately haloalkaliphilic bacterium from a coastal-marine wetland – Mohammad Ali Amoozegar – International Journal of Systematic and Evolutionary Microbiology

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia – Amjad B. Khalil – BioMed Research International

Seasonal dynamics of bacterioplankton community in a large, shallow, highly dynamic freshwater lake – Zhaoyu Kong – Canadian Journal of Microbiology

Sediment microbial communities influenced by cool hydrothermal fluid migration – Laura A. Zinke – Frontiers in Microbiology / Extreme Microbiology

Microbial interactions with dissolved organic matter drive carbon dynamics and community succession’ – Xiaoqin Wu – Frontiers in Microbiology / Microbiological Chemistry and Geomicrobiology

Metabolites change of Scenedesmus obliquus exerted by AgNPs – Pu Wang – Journal of Environmental Sciences

Built environment

Cultivable microbial diversity associated with cellular phones – Rashmi Kurli – Frontiers in Microbiology / Systems Microbiology

Food microbiology

A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods – Marios Mataragas – Food Microbiology

Phages and viruses

Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs – Qiang Wang – Science of The Total Environment

Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States – Qi Chen – Virology Journal

Bioinformatics

Evaluating the use of diversity indices to distinguish between microbial communities with different traits – Sergey Feranchuka – Research in Microbiology

Taxonomic and functional compositions impacted by the quality of metatranscriptomic assemblies – Maggie Lau – Frontiers in Microbiology – Microbiological Chemistry and Geomicrobiology

Biotechnology

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples – Zhichao Zhou – Applied Microbiology and Biotechnology

Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides – Yanan Wang – Biotechnology for Biofuels

Review: A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications – Izzah Shahid – Environmental Sustainability

Microbes in the news

Could we work together with our bacteria to stop infection?

Scientists test bacteria’s power to boost broccoli growth in space

May 10, 2018

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Today we have quite a few interesting papers in “Water microbiome”, there you can read about: drift in the community structuring of bacteria and microbial eukaryotes by R.Logares; phylogeny‐based database “EukRef–Ciliophora” by V. Boscaro;  diverse bacterial and viral populations in agricultural freshwater pond by J. Chopyk. In a “Bioinformatics” section you can read about “MIMOSA: Algorithms for Microbial Profiling” (by O. U. Nalbantoglu) and about use of SplinectomeR package in longitudinal microbiome studies by R.R. Shields- Cutler. Enjoy!

Jobs

PhD position for anaerobic microbiology of the Black Sea, Netherlands

General microbiome

Cargo Transport Shapes the Spatial Organization of a Microbial Community – Abhishek Shrivastava – bioRxiv

The Effect of Berberine on the Transcriptome and Proteome of E. coli – Zhang Shilei – bioRxiv

Predator-by-Environment Interactions Mediate Bacterial Competition in the Dictyostelium discoideum Microbiome – R. Fredrik Inglis – Frontiers in Microbiology / Evolutionary and Genomic Microbiology

Diversity time-period and diversity-time-area relationships exemplified by the human microbiome – Zhanshan (Sam) Ma – Scientific Reports

Pregnancy and early life

Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants – Bing Ma – bioRxiv

Influence of human milk oligosaccharides on adherence of bifidobacteria and clostridia to cell lines – Musilova Sarka  – Acta Microbiologica et Immunologica Hungarica

 

Oral microbiome

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Glycemic Status Affects the Subgingival Microbiome of Diabetic Patients – Priscila Larcher Longo – Journal of Clinical Periodontology

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Human gut microbiome

Fecal microbiota transplantation in experimental ulcerative colitis reveals associated gut microbial and host metabolic reprogramming – Zhixiang Yan – Applied and Environmental Microbiology

Fecal microbiota transplantation treatment for refractory ulcerative colitis with allergy to 5-aminosalicylic acid: A case report – Hong-Gang Wang – Medicine

Review: Influence of Commensal Microbiota on the Enteric Nervous System and Its Role in Neurodegenerative Diseases – Endres K. – Journal of Innate Immunology

Loss of Ethanolamine Utilization in Enterococcus faecalis Increases Gastrointestinal Tract Colonization – Karan Gautam Kavala – mBio

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi – Yan Zhang – mBio

Animal experiments

Effects of gut microbiota and time of treatment on tissue levels of green tea polyphenols in mice – Anna B. Liu – BioFactors

Gastrointestinal microbiota and mucosal immune gene expression in neonatal pigs reared in a cross-fostering model – Nidia Maradiaga – Microbial Pathogenesis

Prolonged restraint stressor exposure in outbred CD-1 mice impacts microbiota, colonic inflammation, and short chain fatty acids – Ross M. Maltz – PLOS One

Review: Biomarkers for monitoring intestinal health in poultry: present status and future perspective – Richard Ducatelle – Veterinary Research

Animal microbiome 

Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae – Ania T. Deutscher – Microbiome

Crown-of-thorns sea star, Acanthaster cf. solaris, have tissue-characteristic microbiomes with potential roles in health and reproduction – Lone Høja – Applied and Environmental Microbiology

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate – Pål Trosvik – Microbiome

Antimicrobial activity in culturable gut microbial communities of springtails – Valeria Agamennone  – Journal of Applied Microbiology

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes – Elizabeth León-Palmero  – PLOS One

Plant, root, and soil microbiome

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Core microbiomes for sustainable agroecosystems – Toju H -Nature Plants

Determination of agricultural impact on soil microbial activity using δ18OP HCl and respiration experiments – Katherine Polain – ACS Earth and Space Chemistry

Seasonal dynamics of bacterial communities in a Betula albosinensis forest – C. Du – European Journal of Soil Science

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Water and extremophile microbiome

Effects of Xiantao sewage treatment on microbial community structure of shallow groundwater in wetland – Shu-Fen Song – bioRxiv

Unexpected versatility in the metabolism and ecophysiology of globally relevant nitrite-oxidizing Nitrotoga bacteria – Andrew Boddicker – bioRxiv

Long-term seasonality of marine photoheterotrophic bacteria reveals low cohesiveness within the different phylogroups – Adrià Auladell – bioRxiv

Molecular cloning of glutathione peroxidase gene of Antarctic ice microalga Chlamydomonas sp. ICE‐L and its expression changes under temperature and salinity stress – Jin Hui Wang – Phycological Research

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes – Ramiro Logares – Environmental Microbiology

EukRef–Ciliophora: A manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates – Vittorio Boscaro – Environmental Microbiology

Novel human-associated Lachnospiraceae genetic markers improve detection of fecal pollution sources in urban waters – Shuchen Feng – Applied and Environmental Microbiology

Municipal wastewater treatment potential and metal accumulation strategies of Colocasia esculenta (L.) Schott and Typha latifolia L. in a constructed wetland – Vivek Rana – Environmental Monitoring and Assessment

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations – Jessica Chopyk – Frontiers in Microbiology / Aquatic Microbiology

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment – Wael S. El-Sayed – Polish Journal of Microbiology

Built environment

Characterization of fungi in office dust: comparing results of microbial secondary metabolites, fungal ITS region sequencing, viable culture, and other microbial indices – Ju Hyeong Park – Indoor Air

Investigation of the Active Biofilm Communities on Polypropylene Filter Media in a Fixed Biofilm Reactor for Wastewater Treatment – Iffat Naz – Journal of Chemical Technology and Biotechnology

Food microbiology

Characterization of the contaminant bacterial communities in sugarcane first-generation industrial ethanol production – Maria L. Bonatelli – FEMS Microbiology Letters

Probiotics / prebiotics

Phylotype-level profiling of lactobacilli in highly complex environments by means of an ITS-based metagenomic approach – Christian Milani – Applied and Environmental Microbiology

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization – Aleksandr A. Arzamasov – Frontiers in Microbiology /Evolutionary and Genomic Microbiology

 

Bioinformatics

MIMOSA: Algorithms for Microbial Profiling – Ozkan Ufuk Nalbantoglu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies – Robin R. Shields-Cutler – Frontiers in Microbiology / Systems Microbiology

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation – Alaine B.Guerra – Environmental Pollution

Biotechnology

Microbial co-culturing systems: butanol production from organic wastes through consolidated bioprocessing – Yujia Jiang – Applied Microbiology and Biotechnology

Techniques

Sensitive detection of Live Escherichia coli by bacteriophage amplification-coupled immunoassay on the Luminex® MAGPIX instrument – Tomotaka Mido – bioRxiv

Microbes in the news

Scientists use dietary seaweed to manipulate gut bacteria in mice

Microbes are savvy investors when contributing to the common good

 

May 4, 2018

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Today we have many interesting news and many papers in “Plant, root, and soil microbiome” section. Enjoy your friday read!

General microbiome

Uncovering the drivers of host-associated microbiota with joint species distribution modeling – Johannes R. Björk – bioRxiv

Competence Inhibition by the XrpA Peptide Encoded Within the comX Gene of Streptococcus mutans – Justin Kaspar – bioRxiv

Microbiota and metabolic diseases – Alessia Pascale – Endocrine

Human respiratory microbiome

The Gut-Lung Axis and Pulmonary Responses to Ozone – Judith A Voynow – American Journal of Respiratory and Molecular Biology

 

Human skin microbiome

Microbial host interactions and impaired wound healing in mice and humans: defining a role for BD14 and NOD2 – Helen Williams – Journal of Investigative Dermatology

Human nearly-sterile sites

The Role of Microbiota in Retinal Disease – Sheldon Rowan – Retinal Degenerative Diseases

Human gut microbiome

Immune Cells and Microbiota Response to Iron Starvation – Marcello Chieppa – Frontiers in Medicine / Gastroenterology

The Role of the Gut Microbiome in Colorectal Cancer – Grace Y. Chen – Clinics in Colon and Rectal Surgery

Enterococcus faecalis AHG0090 is a Genetically Tractable Bacterium and Produces a Secreted Peptidic Bioactive that Suppresses Nuclear Factor Kappa B Activation in Human Gut Epithelial Cells – Páraic Ó Cuív – Frontiers in Immunology /  Microbial Immunology

Animal experiments

Core gut microbiota in Jinhua pigs and its correlation with strain, farm and weaning age – Hua Yang – Journal of Microbiology

Animal microbiome 

Gut microbiomes of wild great apes fluctuate seasonally in response to diet – Allison L. Hicks – Nature Communications

Stochastic processes govern bacterial communities from the blood of pikas and from their arthropod vectors – Huan Li – FEMS Microbiology Ecology

An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods – Sophie J. Krizsan – Ecology & Evolution

The effect of gut microbiota elimination in Drosophila melanogaster: A how-to guide for host–microbiota studies – Chloe Heys  – Ecology & Evolution

Urea hydrolysis by gut bacteria in a hibernating frog: evidence for urea-nitrogen recycling in Amphibia – James M. Wiebler – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm – Ying Zheng – Journal of Microbiology

Soil metabarcoding identifies season indicators and differentiators of pig and Agrostis/Festuca spp. decomposition – Ayodeji O.Olakanye – Forensic Science International

Modulation of plant chemistry by beneficial root microbiota – Desalegn W. Etalo  –  Natural Product Reports

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm – Ying Zheng – Journal of Microbiology

A global atlas of the dominant bacteria found in soil – Manuel Delgado-Baquerizo – Science

Variations of Bacterial Community Diversity Within the Rhizosphere of Three Phylogenetically Related Perennial Shrub Plant Species Across Environmental Gradients – Xiaofan Na –  Frontiers in Microbiology

Combined effects of phosphate-solubilizing bacterium XMT-5 (Rhizobium sp.) and submerged macrophyte Ceratophyllum demersum on phosphorus release in eutrophic lake sediments – Haifeng Li – Environmental Science and Pollution Research

Successful phytoremediation of crude-oil contaminated soil at an oil exploration and production company by plants-bacterial synergism – Kaneez Fatima – International Journal of Phytoremediation

Alginate-perlite encapsulated Pseudomonas putida A (ATCC 12633) cells: preparation, characterization and potential use as plant inoculants – Andrés S. Liffourrena – Journal of Biotechnology

Variations of Bacterial Community Diversity Within the Rhizosphere of Three Phylogenetically Related Perennial Shrub Plant Species Across Environmental Gradients – Xiaofan Na – Frontiers in Microbiology / Terrestrial Microbiology

Water and extremophile microbiome 

Conductive Particles Enable Syntrophic Acetate Oxidation between Geobacter and Methanosarcina from Coastal Sediments – Amelia-Elena Rotaru – mBio

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species – Katharina Fietz – BMC Microbiome

Enhanced degradation of phenol in floating treatment wetlands by plant-bacterial synergism – Hamna Saleem – International Journal of Phytoremediation

Bacterial community diversity in a full scale biofilter treating wastewater odor – M. J. Allievi – Water Science & Technology

Food microbiology

Sausage fermentation and starter cultures in the era of molecular biology methods – Irene Franciosa – International Journal of Food Microbiology

Contribution of the novel sulfur-producing adjunct Lactobacillus nodensis to flavor development in Gouda cheese – Elaine O’Brien – Journal of Dairy Science

Probiotics / prebiotics

Probiotics drive gut microbiome triggering emotional brain signatures – Deepika Bagga – Gut Microbiome

Phages and viruses

Reactivation of latent HIV-1 in vitro using an alcoholic extract from Euphorbia umbellata (Euphorbiaceae) latex – Ana L Valadao – bioRxiv

Mycobacteria recycle their peptidoglycan via a novel pathway which influences antimicrobial resistance and limits proliferation in macrophages – Patrick J. Moynihan – bioRxiv

Biotechnology

Microbiological aspects of thermophile pretreatment of activated sludge inhibiting electricity generation of microbial fuel cell – Yang-Guo Zhao – Water Science & Technology

Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle – Anna Detman – BMC Biotechnology for Biofuels

Microbes in the news 

Researchers find a gene that lets bacteria kill all male flies

Targeting Gut Bacteria to Reduce Disease

Applying live bacteria to skin improves eczema

Walnuts impact gut microbiome and improve health

By wrapping itself in antibodies, this bacterium may become a stable, beneficial part of the gut

A healthy digestive system is all you need in life

 

 

May 2, 2018

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In our 2nd May Digest there are many interesting Jobs, News and papers, among which few recommendations: the review on human oral microbiota by Yangheng Zhang, bacterial versus human thymidylate synthas by Zahidul Islam, gut metabolome meets microbiome by Santosh Lamichhane and GET_PHYLOMARKERS – a new software package for phylogenomics and inferring pan-genome phylogenies. Enjoy!

Jobs

Research assistant in Microbial Systems and Synthetic Biology, University of Amsterdam, the Netherlands

Research Scientist Engineer, University of Washington, WA, US

Post-Doctoral Research Scientist – Molecular Biology/Biochemistry, Rothamsted Research, Harpenden, UK

Post-doc position, Universite Bourgogne Franche-Comté, Dijon, France

General microbiome

Novel Antimicrobials for the Treatment of Clostridium difficile Infection – Nicola Petrosillo – Frontiers in Medicine

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter – Marc Garcia-Garcera – Environmental Microbiology

Further expansion of methane metabolism in the Archaea – Yulin Wang – bioRxiv

Bacterial versus human thymidylate synthase: Kinetics and functionality – Zahidul Islam – PLOS One

Humans as holobionts: implications for prevention and therapy – Maarten van de Guchte – Microbiome

Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales – Shivakumara Siddaramappa – Microbial Genomics

Pregnancy and early life

Spleen development is modulated by neonatal gut microbiota – M. Manuela Rosado – Immunology Letters

HIV antiretroviral exposure in pregnancy induces detrimental placenta vascular changes that are rescued by progesterone supplementation – Hakimeh Mohammadi – Scientific Reports

Human respiratory microbiome

Biological exacerbation clusters demonstrate asthma and COPD overlap with distinct mediator and microbiome profiles  – Michael A. Ghebre – Journal of Allergy and Clinical Immunology

Oral microbiome

Review: Human oral microbiota and its modulation for oral health – Yangheng Zhang – Biomedicine & Pharmacotherapy

Oral Administration of Probiotics Increases Paneth Cells and Intestinal Antimicrobial Activity – Silvia I. Cazorla – Frontiers in Microbiology /Food Microbiology

Oral microbiota reveals signs of acculturation in Mexican American women – Kristi L. Hoffman – PLOS One

Human gut microbiome

Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe – Santosh Lamichhane – Methods

Linking gut microbiota to cardiovascular disease and hypertension: Lessons from chronic kidney disease – B. Meijers – Pharmacological Research

PGRP-LB homolog acts as a negative modulator of immunity in maintaining the gut-microbe symbiosis of red palm weevil, Rhynchophorus ferrugineus Olivier – Bishnu Dawadi – Developmental & Comparative Immunology

Imbalance of gut microbiome and intestinal epithelial barrier dysfunction in cardiovascular disease  – Judith N. Lezutekong – Clinical Science

Intestinal Immunomodulatory Cells (T Lymphocytes): A Bridge between Gut Microbiota and Diabetes – Qingwei Li – Mediators of Inflammation

In Vitro Fermentation Behaviour of Isomalto/Malto‐Polysaccharides Using Human Faecal Inoculum Indicates Prebiotic Potential – Fangjie Gu – Molecular Nutrition & food Research

A repeat offender: Recurrent extraintestinal Clostridium difficile infection following fecal microbiota transplantation – Bradley J.Gardiner – Anaerobe

Illuminating the microbiome’s dark matter: a functional genomic toolkit for the study of human gut Actinobacteria – Jordan E Bisanz – bioRxiv

Animal experiments

Astragalus affects fecal microbial composition of young hens as determined by 16S rRNA sequencing – Hongxing Qiao – AMB Express

Omeprazole Minimally Alters the Fecal Microbial Community in Six Cats: A Pilot Study – Sarah M. Schmid – Frontiers in Veterinary Science

Resveratrol Prevents the Development of Hypertension Programmed by Maternal Plus Post‐Weaning High‐Fructose Consumption Through Modulation of Oxidative Stress, Nutrient‐Sensing Signals, and Gut Microbiota – You-Lin Tain – Molecular Nutrition & Food Research

DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces – Pragathi B. Shridhar – PLOS One

Animal microbiome

Comparative metabolomics of aging in a long-lived bat: Insights into the physiology of extreme longevity – Hope C. Ball – PLOS One

Plant, root, and soil microbiome

Identification of chemotaxis compounds in root exudates and their sensing chemoreceptors in plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 – Haichao Feng – Molecular Plant-Microbe Interactions

Shared strategies for β-lactam catabolism in the soil microbiome – Terence S. Crofts – Nature Chemical Biology

Review: Molecular networks in plant-pathogen holobiont – Tatsuya Nobori – FEBS Letters

Importance of Soil Temperature for the Growth of Temperate Crops under a Tropical Climate and Functional Role of Soil Microbial Diversity – Nurul Syazwani Ahmad Sabri – Microbes and Environments

The Impact of Remediation Through Stabilizing Amendments on Taxonomic and Metabolic Patterns of Bacteria and Archaea in Cadmium-Contaminated Paddy Fields in Southwestern China – Yi Chen – bioRxiv

Cas9/CRISPR genome editing to demonstrate the contribution of Cyp51A Gly138Ser to azole resistance in Aspergillus fumigatus – Takashi Umeyama – bioRxiv

Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment – Heath W. Garris –  PLOS One

Water and extremophile microbiome 

Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile) – Carla G. Leon – PLOS One

The association of diet, gut microbiota and colorectal cancer: what we eat may imply what we get – Jia Yang – Protein & Cell

Marine-influenced microbial communities inhabit terrestrial hot springs on a remote island volcano – Lucy C. Stewart – Extremophiles

Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community – Vitaly V. Kadnikov – Scientific Reports

Effects of Fecal Source Input, Environmental Conditions, and Environmental Sources on Enterococci Concentrations in a Coastal Ecosystem – Derek Rothenheber – bioRxiv

Precipitation of Calcium Carbonate Mineral Induced by Viral Lysis of Cyanobacteria – Hengchao Xu – Biogeosciences

Food microbiology

Probiotic and Technological Properties of Exopolysaccharide Producing Lactic Acid Bacteria Isolated from Cereal-based Nigerian Fermented Food Products – A.T. Adesulu-Dahunsi – Food Control

Phages and viruses

Human enteric bacteria and viruses in five wastewater treatment plants in the Eastern Cape, South Africa – Olayinka Osuolale – Journal of Infection and Public Health

Dissecting the herpesvirus architecture by targeted proteolysis – Gina Rose Daniel – bioRxiv

Bioinformatics

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas – Pablo Vinuesa – Frontiers in Microbiology / Evolutionary and Genomic Microbiology

Bioenergy

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion – Yangyang Jia – Biotechnology for Biofuels

Meta-proteomic analysis of protein expression distinctive to electricity-generating biofilm communities in air-cathode microbial fuel cells – Jeremy F. Chignell – Biotechnology for Biofuels

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants – Julia Hassa – Applied Microbiology and Biotechnology

Mini Review: New concepts in anaerobic digestion processes: recent advances and biological aspects – Antonio Castellano-Hinojosa – Applied Microbiology and Biotechnology

Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution – Chen Chen – PLOS One

Microbes in the news

Microbes living in a toxic volcanic lake could hold clues to life on Mars

Researchers Finally Figure Out How Vaping Impacts Your Gut Bacteria

Bacteria eat antibiotics, and warn each other of threats

 

April 11, 2018

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In today’s digest, check among many interesting articles: the evolution within human microbiome by T.D. Lieberman,  unique microbial biodiversity residing in hadal trenches by L.M. Peoples, changes in community composition in coastal water following exposure to oil and oil dispersant by S.H. Doyle. While in news — a story about “microbial hitchhikers” in restroom hand dryers.

General microbiome

Seven Billion Microcosms: Evolution within Human Microbiomes – Tami D. Lieberman – mSystems

Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead – Benjamin E. Wolfe – mSystems

Understanding Microbiome Stability in a Changing World – Ashley Shade – mSystems

Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation –  Hyaekang Kim – PLOS One

New insight into the early stages of biofilm formation – Catherine R. Armbruster  – PNAS

Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation – Jeronimo Rodriguez-Beltran – Nature Ecology & Evolution

Considering the Lives of Microbes in Microbial Communities – Elizabeth A. Shank – mSystems

Oral microbiome

Inflammatory Bacteriome and Oral Squamous Cell Carcinoma – M. Perera – Journal of Dental Research

Human gut microbiome

The cardiovascular macrophage: a missing link between gut microbiota and cardiovascular diseases? – X. Chen – European Review for Medical and Pharmacological Sciences

Can Diet Influence Our Health by Altering Intestinal Microbiota – Derived Fecal Metabolites? – Qiang Lyu – mSystems

Toward Personalized Control of Human Gut Bacterial Communities – Lawrence A. David – mSystems

Role of the Gut Microbiome in Vertebrate Evolution – Thomas J. Sharpton – mSystems

Dietary nutrition and gut microflora: A promising target for treating diseases – Ying Nie – Trends in Food Science & Technology

Reduction in hepatic secondary bile acids caused by short-term antibiotic-induced dysbiosis decreases mouse serum glucose and triglyceride levels – Takuya Kuno – Scientific Reports

A snapshot of gut microbiota of an adult urban population from Western region of India – Disha Tandon – PLOS One

Animal experiments 

Mice harboring pathobiont-free microbiota do not develop intestinal inflammation that normally results from an innate immune deficiency – Benoit Chassaing – PLOS One

Animal microbiome 

The cultivable autochthonous microbiota of the critically endangered Northern bald ibis (Geronticus eremita) – Joachim Spergser – PLOS One

Plant, root, and soil microbiome

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth – Heather C. Manching –  F1000 Research

Exploring the Potentiality of Novel Rhizospheric Bacterial Strains against the Rice Blast Fungus Magnaporthe oryzae – Narayanappa Amruta –  The Plant Pathology Journal

The sensitivity of soil enzymes, microorganisms and spring wheat to soil contamination with carfentrazone-ethyl – Monika Tomkiel – Journal of Environmental Science and Health, Part B

Water and extremophile microbiome 

Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea, northern China – Mamun Abdullah Al – European Journal of Protistology

Vertically distinct microbial communities in the Mariana and Kermadec trenches – Logan M. Peoples – PLOS One

The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum – Tianyong Zheng – PLOS One

Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy – Shawn E. McGlynn – Applied and Environmental Microbiology

Addressing Confounding Factors in Algal Phosphorus Limitation Experiments – Whitney S. Beck -bioRxiv

Effect of Siderophore on Iron Availability in a Diatom and a Dinoflagellate Species: Contrasting Response in Associated Bacteria – Nicolas Sanchez – Frontiers in Marine Science

Robust Mercury Methylation across Diverse Methanogenic Archaea – Cynthia C. Gilmour – mBio

Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris – Anthony R. Miller – mBio

Trichodesmium physiological ecology and phosphate reduction in the western Tropical South Pacific – Kyle R. Frischkorn – Biogeosciences

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea – Michael F. Graw- Frontiers in Microbiology

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit – Shawn M. Doyle – Frontiers in Microbiology

Understanding Diatom Cell Wall Silicification—Moving Forward – Mark Hildebrand – Frontiers in Marine Science

The hunt for the most-wanted chemolithoautotrophic spookmicrobes – Michiel H in ‘t Zandt – FEMS Microbiology Ecology

Biotechnology

Electron transport chains in organohalide-respiring bacteria and bioremediation implications – Shanquan Wang – Biotechnology Advances

Food microbiology

Listeria monocytogenes strains show large variations in competitive growth in mixed culture biofilms and suspensions with bacteria from food processing environments – Even Heir – International Journal of Food Microbiology

Review: Titanium dioxide (TiO2) photocatalysis technology for nonthermal inactivation of microorganisms in foods – Zhiwei Zhu – Trends in Food Science & Technology

The complexity of wine: clarifying the role of microorganisms – Sophie Tempère – Applied Microbiology and Biotechnology

Probiotics / prebiotics

The effect of Lactobacillus acidophilus and Lactobacillus casei on the in vitro bioaccessibility of flaxseed lignans (Linum usitatissimum L.) – O. Muñoz – Food & Function

The “Golden Age” of Probiotics: A Systematic Review and Meta-Analysis of Randomized and Observational Studies in Preterm Infants – Dermyshi E. – Neonatology

Phages and viruses

Screening of FDA-approved Drugs and Identification of Novel Lassa Virus Entry Inhibitors – Peilin Wang – bioRxiv

Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater – Nichole E. Brinkman – PLOS One

Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus – Piotr M. Skowron – PLOS One

Bioinformatics

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data – Li Chen – PeerJ

Techniques

Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae – Matthew A. Croxen –  Microbial Genomics

Paraffin Embedding and Thin Sectioning of Microbial Colony Biofilms for Microscopic Analysis – William C. Cornell – Journal of Visualized Experiments (Jove)

Microbes in the news 

Bugs, microbes and death can inform the living

Gut bacteria keeps bears healthily obese

Restroom Hand Dryers Are Blowing Bacteria Everywhere

Survival strategy: How one enzyme helps bacteria recover from exposure to antibiotics

Oil-eating bacteria could clean up the next spill

 

March 30, 2018

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In today’s digest you can read a perspective on the social network of microorganisms by Karsten Zengler, a paper on relationship between HIV-1 infection and chronic periodontitis by Tábata Larissa, a paper on sponges-cyanobacteria associations – a global diversity overview by Despoina Konstantinou and/or for an easier read check the report on bacteria in rubber duckies in our ‘News’ section. Enjoy!

Jobs

PhD position Ecology and Evolution of Microbial Infectious Ecosystems, University of Groningen, Groningen, Netherlands

Research Assistant-Post Doc, Karl Landsteiner University of Health Sciences, Krems, Austria

Post-doctoral opportunity at Weill Cornell in New York City, NY, USA

Post Doc Position for Genetic Engineering to Improve Microbial Soluble Expression, BOKU, Vienna, Austria

General microbiome

Perspective: The social network of microorganisms — how auxotrophies shape complex communities – Karsten Zengler – Nature Reviews Microbiology

Intracellular signaling through the comRS system in Streptococcus mutans genetic competence – Simon A.M. Underhill – bioRxiv

Ecological Insights from the Evolutionary History of Microbial Innovations – Mario E Muscarella – bioRxiv

Probing the metabolism of microorganisms – Stilianos Louca – Science

Human respiratory microbiome

Review: Streptococcus pneumoniae: transmission, colonization and invasion – Jeffrey N. Weiser – Nature Reviews Microbiology

Oral microbiome

Relationship between human immunodeficiency virus (HIV-1) infection and chronic periodontitis – Tábata Larissa – Expert Review of Clinical Immunology

Alterations in the oral microbiome in HIV-infected participants after ART administration are influenced by immune status –  Rachel M. Presti – AIDS

Human gut microbiome

A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt – Clinical and Translational Immunology

Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease – Elena Barengolts – PLOS One

Variations in gut microbiota and fecal metabolic phenotype associated with Fenbendazole and Ivermectin Tablets by 16S rRNA gene sequencing and LC/MS-based metabolomics in Amur tiger – Fengping He – Biochemical and Biophysical Research Communications

Single Sampling Versus Multiple Testing Strategy to Assess Gut Microbiota Composition: Does It Matter? – T. G. J. de Meij – Current Microbiology

Scaling Safe Access to Fecal Microbiota Transplantation: Past, Present, and Future – Pratik Panchal – Current Gastroenterology Reports

Fecal Microbiome Among Nursing Home Residents with Advanced Dementia and Clostridium difficile – Rafael Araos – Digestive Diseases and Sciences

Intestinal Metagenomes and Metabolomes in Healthy Young Males: Inactivity and Hypoxia Generated Negative Physiological Symptoms Precede Microbial Dysbiosis – Robert Šket – Frontiers in  Physiology

Intestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases – Maria C. Opazo – Frontiers in Microbiology

Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity – Zachariah DeFilipp – Blood Advances

Animal experiments 

Ecological Restoration of Antibiotic-Disturbed Gastrointestinal Microbiota in Foregut and Hindgut of Cows – Shoukun Ji – Frontiers in Cellular and Infection Microbiology

Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs – T. G. Kiros – Scientific Reports

Oral Antibiotic Treatment of Mice Exacerbates the Disease Severity of Multiple Flavivirus Infections – Larissa B. Thackray – Cell Reports

Animal microbiome 

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali – Benjamin J. Krajacich – PLOS One

A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota – Tao Sun – Scientific Reports

Widespread Elevational Occurrence of Antifungal Bacteria in Andean Amphibians Decimated by Disease: A Complex Role for Skin Symbionts in Defense Against Chytridiomycosis – Alessandro Catenazzi – Frontiers in Microbiology

Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny – Alicia K. Bird – Frontiers in Microbiology

Plant, root, and soil microbiome

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site – José A. Siles – Applied Microbiology and Biotechnology

Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants – Katiúscia Kelli Montanari-Coelho – World Journal of Microbiology and Biotechnology

Response of Nitrifier and Denitrifier Abundance and Microbial Community Structure to Experimental Warming in an Agricultural Ecosystem – Tatoba R. Waghmode – Frontiers in Microbiology

Bacterial diversity and community structure in the rhizosphere of four Ferula species – Xiuling Wang – Scientific Reports

Water and extremophile microbiome

Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean – Despoina Konstantinou – PLOS One

Seasonal variation in the bacterial community composition of a large estuarine reservoir and response to cyanobacterial proliferation – Zheng Xu – Chemosphere

Assessment of Fecal Indicator Bacteria and Potential Pathogen Co-Occurrence at a Shellfish Growing Area – Andrew K. Leight – Frontiers in Microbiology

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin – Min Ren – Frontiers in Microbiology

Carrying Capacity and Colonization Dynamics of Curvibacter in the Hydra Host Habitat – Tanita Wein – Frontiers in Microbiology

Transcriptomic and Ectoine Analysis of Halotolerant Nocardiopsis gilva YIM 90087T Under Salt Stress – Jian Han –  Frontiers in Microbiology

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – Michael W. Henson – The ISME Journal

Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation – Babett Wintsche – Frontiers in Microbiology

Phages and viruses

Review: Autophagy during viral infection — a double-edged sword – Younho Choi – Nature Reviews Microbiology

Viruses in the environment – presence and diversity of bacteriophage and enteric virus populations in the Umhlangane River, Durban, South Africa – Veronna Marie – Journal of Water and Health

Kinetic Modeling of Virus Growth in Cells – John Yin – Microbiology and Molecular Biology Reviews

Bioinformatics

EzMap: a simple pipeline for reproducible analysis of the human virome – Patrick Czeczko  – Bioinformatics

Techniques

Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling – Sajan C.Raju – Journal of Microbiological Methods

Mapping bacteria on filter membranes, an innovative SERS approach – SiyueGao – Journal of Microbiological Methods

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile – Zhirong Li  – Journal of Microbiological Methods

Rapid detection of Klebsiella pneumoniae, Klebsiella oxytoca, Raoultella ornithinolytica and other related bacteria in food by lateral-flow test strip immunoassays – Tatsuya Tominaga –  Journal of Microbiological Methods

Detection of different classes of carbapenemases: Adaptation and assessment of a phenotypic method applied to Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii, and proposal of a new algorithm – Guillaume Gautier – Journal of Microbiological Methods

Rapid detection of carbapenemase-producing Acinetobacter baumannii and carbapenem-resistant Enterobacteriaceae using a bioluminescence-based phenotypic method – Vincent van Almsick – Journal of Microbiological Methods

A quest to find good primers for gene expression analysis of Candida albicans from clinical samples – Gabriela C.Alonso – Journal of Microbiological Methods

Microbes in the news 

The inside of rubber duckies are full of bacteria. You don’t seem surprised

Strings of electron-carrying proteins may hold the secret to ‘electric bacteria’

Researchers develop model to show how bacteria grow in plumbing systems

Harvard scientists uncover an exploitable Achilles’ heel common to most bacteria

Altering Gut Microbiome May Increase Resistance to C. difficile infection

Our Own Microbiome Might Be Triggering The Autoimmune Disease Lupus