Category Archives: Phages and viruses

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 31, 2018

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Today’s Digest features a report that different types of tobacco products can cause oral microbial dysbiosis, an update on fecal microbiome transplant, and exploration into Westernization and evolution of gut microbiota. Enjoy reading!

General microbiology

Alterations of Salmonella Typhimurium Antibiotic Resistance under Environmental Pressure – Mengfei Peng et al. – Applied and Environmental Microbiology

Preprint: Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome – Tabitha Innocent et al. – bioRxiv

Human oral microbiome

Chicken or the Egg: Microbial Alterations in Biopsy Samples of Patients with Oral Potentially Malignant Disorders – Gabor Decsi et al. – Pathology & Oncology Research

** Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study – Yvonne Vallès et al. – Scientific Reports

Human respiratory microbiome

Decreased microbiome diversity in the HIV small airway epithelium – Stella Xu et al. – Respiratory Research

Human gut microbiome

Antibiotic Exposure and Reduced Short Chain Fatty Acid Production after Hematopoietic Stem Cell Transplant – Lindsey ERomick-Rosendale et al. – Biology of Blood and Marrow Transplantation

** Review: Fecal Microbiota Transplantation: Current Status in Treatment of GI and Liver Disease – Byron P.Vaughn et al. – Clinical Gastroenterology and Hepatology

The association between the incidence of intestinal graft-versus-host disease and antibiotic use after allogeneic hematopoietic stem cell transplantation – Daisuke Hidaka et al. – Clinical Transplantation

Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients – Carola Venturini et al. – Intensive Care Medicine Experimental

** Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization – Jacobo de la Cuesta-Zuluaga et al. – Scientific Reports

A diverse range of human gut bacteria have the potential to metabolise the dietary component gallic acid – María Esteban-Torres et al. – Applied and Environmental Microbiology

Metagenomic analysis of gut microbial communities from a Central Asian population – Almagul Kushugulova et al. – BMJ Open

Animal experiments

Early cellular responses of germ-free and specific-pathogen-free mice to Francisella tularensis infection – ZuzanaKrocova et al. – Microbial Pathogenesis

Rat: Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins – Cláudia Marques et al. – Scientific Reports

Mouse: Complementary intestinal mucosa and microbiota responses to caloric restriction – Kalina Duszka et al. – Scientific Reports

Greater Microbial Translocation and Vulnerability to Metabolic Disease in Healthy Aged Female Monkeys – Quentin N. Wilson et al. – Scientific Reports

Medicinal Mushrooms Supplements Alter Chicken Intestinal Microbiome – Janelle Robinson et al. – International Journal of Medicinal Mushrooms

Review: Standardization in host-microbiota interaction studies: challenges, gnotobiology as a tool, and perspective – Catherine Mooser et al. – Current Opinion in Microbiology

Animal microbiome

Review: Where in the serotonergic system does it go wrong? Unravelling the route by which the serotonergic system affects feather pecking in chickens – Elske N.de Haas & Jerine A.J.van der Eijk – Neuroscience & Biobehavioral Reviews

Exploring the pathology of an epidermal disease affecting a circum-Antarctic sea star – Laura Núñez-Pons et al. – Scientific Reports

Assessment of rumen microbiota from a large cattle cohort reveals the pan and core bacteriome contributing to varied phenotypes – Mingyuan Xue et al. – Applied and Environmental Microbiology

Preprint: Whole genome screen reveals a novel relationship between Wolbachia and Drosophila host translation – Yolande Grobler et al. – bioRxiv

Food microbiology

Dynamics and biodiversity of bacterial and yeast communities during the fermentation of cocoa beans – Jatziri Mota-Gutierrez et al. – Applied and Environmental Microbiology

Plant, root and soil microbiome

Alternate life history phases of a common seaweed have distinct microbial surface communities – Matthew A Lemay et al. – Molecular Ecology

Diversity of bacterial microbiota of coastal halophyte Limonium sinense and amelioration of salinity stress damage by symbiotic plant growth-promoting actinobacterium Glutamicibacter halophytocola KLBMP 5180 – Sheng Qin et al. – Applied and Environmental Microbiology

Bacterial microbiota protect an invasive bark beetle from a pine defensive compound – Chihang Cheng et al. – Microbiome

Structural inflexibility of the rhizosphere microbiome in mangrove plant Kandelia obovata under elevated CO2 – Panqing Yin et al. – Marine Environmental Research

Mutualistic fungus Phomopsis liquidambari increases root aerenchyma formation through auxin-mediated ethylene accumulation in rice (Oryza sativa L.) – Li-Yan Hu et al. – Plant Physiology and Biochemistry

Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient – Ming Ma et al. – Science of The Total Environment

Isolation and diversity of culturable rhizobacteria associated with economically important crops and uncultivated plants in Québec, Canada – Di Fan et al. – Systematic and Applied Microbiology

Phages and viruses

Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron – Yvan Bettarel et al. – Scientific Reports

Bioinformatics

Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity – Anton Bankevich & Pavel A.Pevzner – Cell Systems

Microbes in the news

Gut bacteria can protect against Salmonella infections – Press Trust of India – Business Standard

July 26, 2018

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Altered intestinal phage populations in murine colitis, degradation of aromatic compounds by the wheat rhizosphere, barley products change the gut microbiota composition of rats.

General microbiome

Defining microbiome function – Jonathan L Klassen – Nature Microbiology

Electroactive microorganisms and microbial consortia – Enrico Marsili – Bioelectrochemistry

Humanome Versus Microbiome: Games of Dominance and Pan-Biosurveillance in the Omics Universe – Manousos E Kambouris – OMICS: A Journal of Integrative Biology

Human respiratory microbiome

The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens – Sophie Edouard – European Journal of Clinical Microbiology & Infectious Diseases

Human oral microbiome

Paired analysis of the microbiota between surface tissue swabs and biopsies from pediatric patients undergoing adenotonsillectomy – James Johnston – International Journal of Pediatric Otorhinolaryngology

Bacterial endotoxins and microorganisms in the oral cavities of patients on cancer therapy – J Mathews – Microbial Pathogenesis

Human gut microbiome

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface – Marta Calatayud Arroyo – Journal of Visualized Experiments

Altered gut microbiota profile in patients with generalized anxiety disorder – Hai-yin Jiang – Journal of Psychiatric Research

Animal experiments

Beneficial changes of gut microbiota and metabolism in weaned rats with Lactobacillus acidophilus NCFM and Bifidobacterium lactis Bi-07 supplementation – Mengxia Wang – Journal of Functional Foods

Diammonium Glycyrrhizinate Protects against Non-Alcoholic Fatty Liver Disease in mice through modulation of gut microbiota and restoring intestinal barrier – Yun Li – Molecular Pharmaceuticals

Animal microbiome

Altering the Gut Microbiome of Cattle: Considerations of Host-Microbiome Interactions for Persistent Microbiome Manipulation – Brooke A Clemmons – Microbial Ecology

Plant, root, and soil microbiome

Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest – Julia C Haas – Soil Biology and Biochemistry

Diversity and Co-occurrence Patterns of Soil Bacterial and Fungal Communities in Seven Intercropping Systems – Sen Li – Frontiers in Microbiology

Metatranscriptome Analysis Deciphers Multifunctional Genes and Enzymes Linked With the Degradation of Aromatic Compounds and Pesticides in the Wheat Rhizosphere – Dhananjaya P Singh – Frontiers in Microbiology

Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population – Lucas Dantas Lopes – Environmental Microbiology

Water and extremophile microbiome

Comparative microbial communities in tidal flats sediment on Incheon, South Korea – Hye Jin Choi – The Journal of General and Applied Microbiology

Food microbiology

Fucoidan alleviates dyslipidemia and modulates gut microbiota in high-fat diet-induced mice – Min Liu – Journal of Functional Foods

Polyphenolic derivatives from mango (Mangifera Indica L.) modulate fecal microbiome, short-chain fatty acids production and the HDAC1/AMPK/LC3 axis in rats with DSS-induced colitis – Hyemee Kim – Journal of Functional Foods

Jaboticaba berry peel intake increases short chain fatty acids production and prevent hepatic steatosis in mice fed high-fat diet – Ângela Giovana Batista – Journal of Functional Foods

Bioavailability of Isoflavone Metabolites After Korean Fermented Soybean Paste (Doenjang) Ingestion in Estrogen‐Deficient Rats – Da-Hye Lee – Journal of Food Science

Barley Products of Different Fibre Composition Selectively Change Microbiota Composition in Rats – Cristina Teixeira – Molecular Nutrition & Food Research

Probiotics/prebiotics

A soy-based probiotic drink modulates the microbiota and reduces body weight gain in diet-induced obese mice – Juliana de Carvalho Marchesin – Journal of Functional Foods

Probiotics in cystic fibrosis patients: A double blind crossover placebo controlled study: Pilot study from the ESPGHAN Working Group on Pancreas/CF – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Probiotics in Pediatric Gastroenterology: Emerging Indications – Elena Scarpato – Journal of Clinical Gastroenterology

Phages and viruses

Murine colitis reveals a disease-associated bacteriophage community – Breck A Duerkop – Nature Microbiology

Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins – Alexander P Hynes – Nature Communications

Bioinformatics

A marginalized two-part Beta regression model for microbiome compositional data – Haitao Chai – PLOS Computational Biology

Metabolomics

Simultaneous HS-SPME GC-MS determination of short chain fatty acids, trimethylamine and trimethylamine N-oxide for gut microbiota metabolic profile – Jessica Fiori – Talanta

Techniques

Balances: a New Perspective for Microbiome Analysis – J Rivera-Pinto – mSystems

Coupling magnetic-nanoparticle mediated isolation (MMI) and stable isotope probing (SIP) for identifying and isolating the active microbes involved in phenanthrene degradation in wastewater with higher resolution and accuracy – Jibing Li – Water Research

July 25, 2018

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Today’s digest consists of opinion paper from European MyNewGut project, review article on gut microbiota dysbiosis, and meta-analysis to find association between antibiotic associated microbiota perturbation and childhood obesity. Also includes application of contraceptive rings and probiotic capsules to increase vaginal lactobacilli, and how preprint publishing could create confusion in public journalism!

General microbiome

Towards microbiome-informed dietary recommendations for promoting metabolic and mental health: Opinion papers of the MyNewGut project – Yolanda Sanz – Clinical Nutrition

Review: The gut microbiota: A new target in the management of alcohol dependence? – Sophie Leclercq – Alcohol

Review: Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery – Michael Kriss – Current Opinion in Microbiology

Review: Environmental factors, gut microbiota, and colorectal cancer prevention – Mingyang Song – Clinical Gastroenterology and Hepatology

Review: The association between antibiotic use in infancy and childhood overweight or obesity: a systematic review and meta-analysis – SA Miller – Obesity Reviews

Multi-site human microbiome

Unique subgingival microbiota associated with periodontitis in cirrhosis patients – Anders Jensen – Scientific Reports

Human respiratory microbiome

A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota – Katrina Kalantar – bioRxiv

Human vaginal microbiome

Contraceptive rings promote vaginal lactobacilli in a high bacterial vaginosis prevalence population: A randomised, open-label longitudinal study in Rwandan women – Tania Crucitti – PlosOne

Comparative phase I randomized open-label pilot clinical trial of Gynophilus® (Lcr regenerans®) immediate release capsules versus slow release muco-adhesive tablets – Caroline Dausset – European Journal of Clinical Microbiology and Infectious Diseases

Human gut microbiome

Association Between Intestinal Microbiota Collected at Hospital Admission and Outcomes of Patients with Cirrhosis – Jasmohan S Bajaj – Clinical Gastroenterology and Hepatology

Animal experiments

Butyrate regulates inflammatory cytokine expression without affecting oxidative respiration in primary astrocytes from spontaneously hypertensive rats – Tao Yang – Physiological Reports

Plant, root, and soil microbiome

Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA – Katerina Papp – The ISME Journal

Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil – Gylaine VT Tchakounte – Microbiological Research

Water and extremophile microbiome

Effects of mercury addition on microbial community composition and nitrate removal inside permeable reactive barriers – Kenly Hiller-Bittrolff – Environmental Pollution

Food microbiology

Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems – Clemence Defois – Scientific Reports

Polyol-producing lactic acid bacteria isolated from sourdough and their application to reduce sugar in a quinoa-based milk substitute – Stephanie Jeske – International Journal of Food Microbiology

Probiotics / prebiotics

Probiotics in cystic fibrosis patients: A double blind crossover placebo controlled study: Pilot study from the ESPGHAN Working Group on Pancreas/CF – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Phages and viruses

Parvovirus Minute Virus of Mice Interacts with Sites of Cellular DNA Damage to Establish and Amplify its Lytic Infection – Kinjal Majumder – eLife

Techniques

Review: The evolving interface between synthetic biology and functional metagenomics – Eric Van der Helm – Nature Chemical Biology

Targeted analysis of microbial-generated phenolic acid metabolites derived from grape flavanols by gas chromatography-triple quadrupole mass spectrometry – Eileen Carry – Journal of Pharmaceutical and Biomedical Analysis

Science, publishing, and career 

Preprints could promote confusion and distortion – Nature News

‘Science-adjacent’ conferences and why they matter – Nature News

Tulika’s non-microbiology picks

Metformin inhibits gluconeogenesis via a redox-dependent mechanism in vivo – Anila K Madiraju – Nature Medicine

 

July 22, 2018

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Soil microbial community structure during pedogenesis; microbes in forest ecosystem; microbes of turbid Korean wines, of Mexican cheese; evaluating genomic diversity of viruses using a common bioinformatics platform and a lot more for today’s digest.

General microbiome

Nature’s conductors: what can microbial multi-heme cytochromes teach us about electron transport and biological energy conversion? – Grace W Chong – Current Opinion in Chemical Biology

Proteins of generalist and specialist pathogens differ in their amino acid composition – Luz P Blanco – Life Science Alliance

Human gut microbiome

Inhibiting Growth of Clostridioides difficile by Restoring Valerate, Produced by the Intestinal Microbiota – Julie A.K. McDonald – Gastroenterology

Animal experiments 

Bifidobacterium pseudolongum in the Ceca of Rats Fed Hi-Maize Starch Has Characteristics of a Keystone Species in Bifidobacterial Blooms – Manuela Centanni – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial Compositions and Enzymes of a Forest Ecosystem in Alabama: Initial Response to Thinning and Burning Management Selections – Fritz A. Ntoko – Open Journal of Forestry

Changes in soil microbial community structure in relation to plant succession and soil properties during 4000 years of pedogenesis – Shankar G. Shanmugam – European Journal of Soil Biology

Microbial Diversities and Potential Hazards of Korean Turbid Rice Wines (makgeolli): Multivariate Analyses – Nam Hee Kim – Food Microbiology

Impact of the South-to-North water diversion on the soil microbial community structure in the Miyun Reservoir riparian zone – Jiangqi Qu – IOP Science

The soil microbial foodweb revisited with metatranscriptomics – predatory Myxobacteria as keystone taxon? – Sebastian Petters – bioRxiv

Built environment 

Black water collected from the septic tank treated with a living machine system: HRT effect and microbial community structure – Zhan Jin – Chemosphere

Microbial communities and functional genes of nitrogen cycling in an electrolysis augmented constructed wetland treating wastewater treatment plant effluent – Pengfei Zhang –  Chemosphere

Food microbiology

Profiling of bacterial and fungal communities of Mexican cheeses by high throughput DNA sequencing – Selvasankar Murugesan – Food Research International

Phages and viruses

Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy – Pakorn Aiewsakun -Journal of General Virology

Techniques

Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus – Chan Yeong Kim – Scientific Reports

Environmental proteomic studies: closer step to understand bacterial biofilms – Anupama Rani – World Journal of Microbiology and Biotechnology

Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments – Muhammad Bilal – Applied Microbiology and Biotechnology

A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities – Mehreen Anjum – Journal of Microbiological Methods

 

July 12, 2018

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Bacteria in desert soils, mycobacteria in showerhead biofilms, metabolic diversity of microbes from commercial probiotics.

Human gut microbiome

Pre-print: Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics – Ravi Ranjan – bioRxiv

Animal microbiome

Pre-print: Olive fruit fly rearing procedures affect the vertical transmission of the bacterial symbiont Candidatus Erwinia dacicola – Patrizia Sacchetti – bioRxiv

Pre-print: Survey of bacteria associated with western corn rootworm life stages reveals no difference between insects reared in different soils – Dalton C Ludwick – bioRxiv

Plant, root, and soil microbiome

Influences of fertilization on soil environment and microorganism in continuous cropping based on high-throughput sequencing – Zhang YiJie – Journal of Agricultural Science and Technology

Review: Consortia of cyanobacteria/microalgae and bacteria in desert soils: an underexplored microbiota – Isiri Perera – Applied Microbiology and Biotechnology

Effects of cover crop in an apple orchard on microbial community composition, networks, and potential genes involved with degradation of crop residues in soil – Wei Zheng – Biology and Fertility of Soils

Microbial Community Level Physiological Profiles of Active Mud Volcano Soils in Andaman and Nicobar Islands – N Amaresan – National Academy Science Letters

Water and extremophile microbiome

Pre-print: Interspecies interactions mediated by conductive minerals in the sediments of the ferruginous Lake La Cruz, Spain – Amelia-Elena Rotaru – bioRxiv

Pre-print: Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes – Dean J Horton – bioRxiv

Pre-print: Hidden in plain sight – highly abundant and diverse planktonic freshwater Chloroflexi – Maliheh Mehrshad – bioRxiv

Built environment

Pre-print: Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health – Matthew Gebert – bioRxiv

Probiotics/prebiotics

Pre-print: Metabolic diversity of bacteria and yeast from commercial probiotic products illustrated by phenotypic profiling – Juliana Mastronunzio Ansari – bioRxiv

Phages and viruses

Pre-print: Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow – Antonin Bal – bioRxiv

More microbes

Species-specific activity of antibacterial drug combinations – Ana Rita Brochado – Nature

Science, career, and publishing

Hot streaks in artistic, cultural, and scientific careers – Lu Liu – Nature

Amy’s non-microbiology picks

Reprogramming human T cell function and specificity with non-viral genome targeting – Theodore L Roth – Nature

11 July, 2018

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Today’s digest is short but full of exciting research. Firstly, a look at how maternal diet can influence infant microbiome and a brilliant preprint highlighting the role women have played in science

General Microbiome

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Lundgren SN. Microbiome.

Oral Microbiome

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease.Kazumichi Abe. PLos ONE

Gut Microbiome

Gut microbiota-immune-brain interactions in chemotherapy-associated behavioral comorbidities.Jordan KR Cancer

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas. Das B. Scientific Reports

Commentary:Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis.Agustí G. Frontier in Cellular and Infection Microbiology .

Animal Experiments and Microbiome

Non-nutritive sweeteners possess a bacteriostatic effect and alter gut microbiota in mice.Wang. PLoS One

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria. Ge Y. PLoS Neglected Tropical Diseases

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria.Pais IS. PLoS Biology

Plant, Soil, and Water Microbiome

Microbial community of tannery wastewater involved in nitrification revealed by Illumina MiSeq sequencing.Ma X. Journal of Microbiology and Biotechnology

Rhizosphere fungal community dynamics associated with Rehmannia glutinosa replant disease in a consecutive monoculture regime. Wu L Phytopathology.

Effects of soil erosion on agro-ecosystem services and soil functions: A multidisciplinary study in nineteen organically farmed European and Turkish vineyards. Costantini EAC. Journal of Environmental Management

Virome

Temporal dynamics of the lung and plasma viromes in lung transplant recipients Maia Segura-Wang. PLos ONE

Techniques

Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in <i>Escherichia coli</i>.Westmann CA. Frontier in Microbiology.

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies.Lau MCY. Frontiers in Microbiology.

Preprint

Illuminating women’s hidden contribution to the foundation of theoretical population genetics. Samantha Dung. bioRxiv

July 9, 2018

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Today’s Digest features new insights into the microbial communities associated with shisha (water pipe), microbial mats, and tropical marine ecosystems. In addition, there are some new techniques and benchmarks to read about, including domain intelligible models for mining ‘omics data and the potential of giant viruses to introduce errors into metagenomic binning. I also highlighted some non-microbiology picks about the potential role for robots in autism therapies and photographs of a brand new planet taken at the Max Planck Institute for Astronomy!

Human gut microbiome
Faecal microbiota transplantation alters gut microbiota in patients with irritable bowel syndrome: results from a randomised, double-blind placebo-controlled study – Sofie Ingdam Halkjær – Gut

Animal experiments
Early-life sickness may predispose Siberian hamsters to behavioral changes following alterations of the gut microbiome in adulthood – Kristyn E. Sylvia – Brain, Behavior, and Immunity

Deficiency in class III PI3-kinase confers postnatal lethality with IBD-like features in zebrafish – Shaoyang Zhao – Nature Communications

Plant, root, and soil microbiome
Shisha microbiota: the good, the bad and the not so ugly – Julia Hani – BMC Research Notes

Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes – Hon Lun Wong – The ISME Journal

Water and extremophile microbiome
A long-standing complex tropical dipole shapes marine microbial biogeography – Wei Yan – Applied and Environmental Microbiology

Probiotics / prebiotics
Probiotic Lactobacillus paracasei HII01 protects rats against obese-insulin resistance-induced kidney injury and impaired renal organic anion transporter 3 (Oat3) function – Keerati Wanchai – Clinical Science

Bioinformatics
Domain Intelligible Models – Sultan Imangaliyev – Methods

Techniques
Metagenomic binning reconstruction coupled with automatic pipeline annotation and giant viruses: a potential source of mistake in annotations – Julien Andreani – Virus Research

Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds? – Vaibhav Diwan – Journal of Microbiological Methods

Linking uncultivated microbial populations with benthic carbon turnover using quantitative stable isotope probing – Ömer K. Coskun – Applied and Environmental Microbiology

Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS) – Kasia Piwosz – The ISME Journal

Alyson’s non-microbiology picks
Personalized machine learning for robot perception of affect and engagement in autism therapy – Ognjen Rudovic – Science Robotics

Scientists Capture First Birth Of A Planet – M. Keppler – via NPR

July 04, 2018

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Today’s Digest is about association of the microbiome at various mucosal sites with different diseases in humans, germ-free chicken and microbial community in anoxic inter-tidal zone of Earth to study Lacustrine system of Mars. You can also read about BacStalk- software to analyze bacterial images, Chinese baby project and how air pollution is contributing to incidence of diabetes.

General microbiome

Review: Gut associated bacteria are critical to metabolism, inflammation and health – Philip Newsholme – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The Microbiome and Acute Kidney Injury – H Rabb – Nephron

Multi-site human microbiome

Review: Cariogenic microbiome and microbiota of the early primary dentition: a contemporary overview – Kausar Sadia Fakhruddin – Oral Diseases

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease – Kazumichi Abe – PlosOne

Human respiratory microbiome

Severe Obstructive Sleep Apnea is Associated with Alterations in the Nasal Microbiome and Increase in Inflammation – Benjamin G Wu – American Journal of Respiratory and Critical Care Medicine

Microbiota Composition and the Integration of Exogenous and Endogenous Signals in Reactive Nasal Inflammation – Francesco Antonio Salzano – Journal of Immunology Research

Human skin microbiome

Inflammatory cytokines and biofilm production sustain Staphylococcus aureus outgrowth and persistence: a pivotal interplay in the pathogenesis of Atopic Dermatitis – E.G.Di Domenico – Scientific reports

Human vaginal microbiome

Complex ecological interactions of Staphylococcus aureus in tampons during menstruation – Isaline Jacquemond – Scientific Reports

Human gut microbiome

Altered Intestinal Microbiota with Increased Abundance of Prevotella Is Associated with High Risk of Diarrhea-Predominant Irritable Bowel Syndrome – Tingting Su – Gastroenterology Research and Practice

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients – Bahtiyar Yilmaz – PlosOne

Animal experiments 

Gut Microbial succession during conventionalization of germfree chicken – Thomas Milton – bioRxiv

Early-life antibiotics attenuate regulatory T cell generation and increase the severity of murine house dust mite-induced asthma – Alexander J. Adami – Pediatric Research

Changes in intestinal gene expression and microbiota composition during late pregnancy are mouse strain dependent – Marlies Elderman – Scientific Reports

Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism – Catherine R. Lammert – The Journal of Immunology

Plant, root, and soil microbiome

Cascading effects of elevated ozone on wheat rhizosphere microbial communities depend on temperature and cultivar sensitivity – F. Changey – Environmental Pollution

Litter quality drives the differentiation of microbial communities in the litter horizon across an alpine treeline ecotone in the eastern Tibetan Plateau – Haifeng Zheng – Scientific Reports

Identification of a Novel Feruloyl Esterase by Functional Screening of a Soil Metagenomic Library – Xuanxuan Li – Applied Biochemistry and Biotechnology

Water and extremophile microbiome

Quorum sensing and iron regulate a two-for-one siderophore gene cluster in Vibrio harveyi – Darcy L. McRose – PNAS

Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals – Alexey Vorobev – Environmental Microbiology

Metabolic potential of microbial communities from ferruginous sediments – Aurele Vuillemin – Environmental Microbiology

Microbes in space

The Microbial Community of a Terrestrial Anoxic Inter-Tidal Zone: A Model for Laboratory-Based Studies of Potentially Habitable Ancient Lacustrine Systems on Mars – Elliot Curtis-Harper – Microorganisms

Phages and viruses

Development of a high-throughput assay to detect antibody inhibition of low pH induced conformational changes of influenza virus hemagglutinin – Jessica F. Trost – PlosOne

Techniques

Review: Errors during Gene Expression: Single-Cell Heterogeneity, Stress Resistance, and Microbe-Host Interactions – Christpher R. Evans – mBio

BacStalk: a comprehensive and interactive image analysis software tool for bacterial cell biology – Raimo Hartmann – bioRxiv

Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Microbes in the news

Bacteria can ‘divide and conquer’ to vanquish their enemies – Science Daily

Gigantic study of Chinese babies yields slew of health data – Nature News

Non-microbiology picks

The 2016 global and national burden of diabetes mellitus attributable to PM2·5 air pollution – Benjamin Bowe – The Lancet Planetary Health

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