Category Archives: General Microbiome

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

 

June 18, 2018

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Have a good Monday! Today in Microbiome Digest: reviews about the relationship between microbiome and brain function, vaccine response and dermatology. Studies about psoriasis and the gut microbiology, the effect of osmotic changes on the gut microbiota, protocols for oral microbiota profiling in lab classes, the role of indole in gut inflammation and more…

Human and General Microbiome

Review: Bile acids and FXR in functional gastrointestinal disorders – Paula Mosińska – Digestive and Liver Disease

Review: The Microbiome in Psychology and Cognitive Neuroscience – Amar Sarkar – Trends in Cognitive Sciences

Review: The influence of the intestinal microbiome on vaccine responses – Petra Zimmermann – Vaccine

Review: Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity – Eric C. Keen – Trends in Microbiology

The microbiome in dermatology – Shenara Musthaq – Clinics in Dermatology

Is psoriasis a bowel disease? Successful treatment with bile acids and bioflavonoids suggests it is – P. Haines Ely – Clinics in Dermatology

Microbial markers in colorectal cancer detection and/or prognosis – Romain Villéger – World Journal of Gastroenterology

Neurotransmitter modulation by the gut microbiota – Philip Strandwitz – Brain Research

Intestinal microbiota assessment in cirrhotic patients from a Mexican mestizo population – C. Pérez-Monter – Revista de Gastroenterología de México (Article in Spanish)

Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China – Peng Wu – Frontiers in Cellular and Infection Microbiology

Analysis of human C24 bile acids metabolome in serum and urine based on enzyme digestion of conjugated bile acids and LC-MS determination of unconjugated bile acids – Pingping Zhu – Analytical and Bioanalytical Chemistry

Tobacco-smoking-related prevalence of methanogens in the oral fluid microbiota – Ghiles Grine – Scientific Reports

Effect of rectal douching/enema on rectal gonorrhoea and chlamydia among a cohort of men who have sex with men on HIV pre-exposure prophylaxis – Adiba Hassan – Sexually Transmitted Infections

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

The urinary microbiome in women with mixed urinary incontinence compared to similarly aged controls – Yuko M. Komesu – International Urogynecology Journal

The influence of in vitro pectin fermentation on the human fecal microbiome – So-Jung Bang – AMB Express

Host genetics and microbiome associations through the lens of genome wide association studies – Omer Weissbrod – Current Opinion in Microbiology

Cutibacterium acnes and the shoulder microbiome – Boyang Qiu – Journal of Shoulder and Elbow Surgery

 

Animal Microbiome / Animal Experiments

Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota – Carolina Tropini – Cell

Probiotics L. acidophilus and B. clausii Modulate Gut Microbiota in Th1- and Th2-Biased Mice to Ameliorate Salmonella Typhimurium-Induced Diarrhea – Biswaranjan Pradhan – Probiotics and Antimicrobial Proteins

Altered microRNA regulation of short chain fatty acid receptors in the hypertensive kidney is normalized with hydrogen sulfide supplementation – Gregory J. Weber – Pharmacological Research

The effect of antibiotics on social aversion following early life inflammation – Amanda C. Kentner – Physiology & Behavior

Analysis of the Gut Microbial Diversity of Dairy Cows During Peak Lactation by PacBio Single-Molecule Real-Time (SMRT) Sequencing – Weicheng Li – Current Microbiology

Diet Modifies Colonic Microbiota and CD4+ T Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-cell Expression of Interleukin 23 – Lili Chen – Gastroenterology

Chronic exposure to fungicide propamocarb induces bile acid metabolic disorder and increases trimethylamine in C57BL/6J mice – Sisheng Wu – Science of The Total Environment

Distribution of Salmonella Enteritidis in internal organs and variation of cecum microbiota in chicken after oral challenge – Jinxin Zeng – Microbial Pathogenesis

The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut – Korin Albert – Microbial Genomics

The gut microbiota metabolite indole alleviates liver inflammation in mice – Martin Beaumont – The FASEB Journal

Alpha-Ketoglutarate in Low-Protein Diets for Growing Pigs: Effects on Cecal Microbial Communities and Parameters of Microbial Metabolism – Jiashun Chen – Frontiers in Microbiology

Berberine Regulates Treg/Th17 Balance to Treat Ulcerative Colitis Through Modulating the Gut Microbiota in the Colon

Screening of multimeric β-xylosidases from the gut microbiome of a higher termite, Globitermes brachycerastes – Huantian Cui – Frontiers in Pharmacology

Impact of Gut Microbiota and Diet on the Development of Atherosclerosis in Apoe-/- Mice – Annika Lindskog Jonsson – Arteriosclerosis, Thrombosis, and Vascular Biology

Saturated long-chain fatty acid-producing bacteria contribute to enhanced colonic motility in rats – Ling Zhao – Microbiome

News in Brief: Antibiotics Protect Against Liver Tumors in Mice in Cancer Discovery

 

Water Microbiome

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass – Justus Hardegen – Bioresource Technology

 

Protocols and Methodologies

Simple Protocol for Molecular Fingerprinting of Human Oral Microbiota Samples in Lab Classes – Ana C. Henriques – Journal of Microbiology & Biology Education

Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls – Dieter M. Tourlousse – Scientific Reports

Taxonomy-aware feature engineering for microbiome classification – Mai Oudah – BMC Bioinformatics

 

June 14, 2018

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Microbial inhabitants of chimpanzee beds, the California cat flea microbiome, butterfly-associated bacterial communities.

General microbiome

Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations – Stefan Vet – PLOS ONE

Multi-site human microbiome

Review: The interaction between iNKT cells and the mucosal microbiota – Fatma Zehra Hapil – Immunology

Human skin microbiome

Cutibacterium acnes (Propionibacterium acnes) and acne vulgaris: a brief look at the latest updates – B Dréno – Journal of the European Academy of Dermatology and Venereology

Human gut microbiome

Review: Gut dysbiosis: a potential link between increased cancer risk in ageing and inflammaging – Arya Biragyn – The Lancet Oncology

The microbiome of translocated bacterial populations in patients with and without inflammatory bowel disease – Christopher John Kiely – Internal Medicine Journal

Animal experiments

Oxaliplatin-induced changes in microbiota, TLR4+ cells and enhanced HMGB1 expression in the murine colon – Vanesa Stojanovska – PLOS ONE

Bifidobacteria attenuate the development of metabolic disorders, with inter- and intra-species differences – Guangsu Zhu – Food & Function

Immunomodulation and effects on microbiota after in ovo administration of chicken cathelicidin-2 – Tryntsje Cuperus – PLOS ONE

Animal microbiome

Apparent Total Tract Macronutrient Digestibility, Serum Chemistry, Urinalysis, and Fecal Characteristics, Metabolites and Microbiota of Adult Dogs Fed Extruded, Mildly Cooked, and Raw Diets – Kiley M Algya – Journal of Animal Science

Assessing Cat Flea Microbiomes in Northern and Southern California by 16S rRNA Next-Generation Sequencing – Elton J R Vasconcelos – Vector-Bronze and Zoonotic Diseases

Pre-print: High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas – César A Cárdenas – PeerJ

Synchronized shift of oral, faecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction – Muriel Dietrich – Royal Society Open Science

Dietary and developmental shifts in butterfly-associated bacterial communities – Kruttika Phalnikar – Royal Society Open Science

Plant, root, and soil microbiome

Impact of pyrometallurgical slags on sunflower growth, metal accumulation and rhizosphere microbial communities – A C Agnello – Chemosphere

Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures – Daniel R Lammel – Microbiome

Review: A three-act play: pentachlorophenol threats to the cork oak forest soils mycobiome – Adélia Varela – Current Opinion in Microbiology

Soil homogenization and microedges: perspectives on soil‐based drivers of plant diversity and ecosystem processes – Holly J Stover – Ecosphere

Soils beneath different arctic shrubs have contrasting responses to a natural gradient in temperature – Qiong Zhao – Ecosphere

Effects of straw return on bacterial communities in a wheat-maize rotation system in the North China Plain – Dali Yu – PLOS ONE

Pre-print: Convergent gain and loss of genomic islands drives lifestyle changes in plant-associated bacteria – Ryan A Melnyk – bioRxiv

Water and extremophile microbiome

Vertical and horizontal biogeographic patterns and major factors affecting bacterial communities in the open South China Sea – Yi Li – Scientific Reports

Built environment

Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds – Megan S Thoemmes – Royal Society Open Science

Bacteria art

Creative Culture: Bacterial Art Project Combines Art and Science – Candice Dyer – Brenau Window Online

Science, career, and publishing

Bioinformatics core competencies for undergraduate life sciences education – Melissa A Wilson Sayres – PLOS ONE

Pre-print: Outcomes of early NIH-funded investigators: Experience of the National Institute of Allergy and Infectious Diseases – Patricia A Haggerty – bioRxiv

June 13, 2018

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Events and jobs

Computational scientists (from post-master to postdoc fellowships) in metagenomics and microbial genomics : Trento, Italy – The Laboratory of Computational Metagenomics

General microbiome

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative – Jun Wang, Microbiome Announcement

Microbial ecology

Everything is not everywhere: a tale on the biogeography of cyanobacteria – Karine Felix Ribeiro, Hydrobiologia

A Meta‐Analysis of Temperature Sensitivity as a Microbial Trait – Charlotte J. Alster, Global Change Biology

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities – John Davison, ISME

Bacillus thuringiensis produces the lipopeptide thumolycin to antagonize microbes and nematodes – Dehong Zheng, Microbiological Research

Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity – Ambrin Sarwar, Plos One

Antarctic cryptoendolithic fungal communities are highly adapted and dominated by Lecanoromycetes and Dothideomycetes – Claudia Coleine, Frontiers in Microbiology

Pregnancy and early life

The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis – Stephen Wandro, mSphere

The role of breast milk in the colonization of neonatal gut and skin with coagulase-negative staphylococci – Hiie Soeorg, Pediatric Research

Multisite human microbiome

Prion-like Propagation of α-synuclein in the gut-brain axis – Ying Chen, Brain Research Bulletin

Microbiome-Gut-Brain Axis and Toll-Like Receptors in Parkinson’s Disease – Valentina Caputi, International Journal of Molecular Sciences

Current Insights in Microbiome Shifts in Sjogren’s Syndrome and Possible Therapeutic Interventions – Christina Tsigalou, Frontiers in Immunology

Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome between Neonatal Intensive Care Unit (NICU) Environments – Suchitra K. Hourigan, Frontiers in Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood, Scientific Reports

Cutibacterium acnes (Propionibacterium acnes) and acne vulgaris: a brief look at the latest updates – B. Dréno, Journal of the European Academy of Dermatology and Venereology

Characterisation of Cutibacterium acnes phylotypes in acne and in vivo exploratory evaluation of Myrtacine® – S. Pécastaings, Journal of the European Academy of Dermatology and Venereology

Human oral microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise  Tornavoi de Castro, Archives of Oral Biology

Genetic Association with Subgingival Bacterial Colonization in Chronic Periodontitis – Franco Cavalla, Genes

Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK – Andrew G Farrer, bioRxiv

Human gut microbiome

Breath methane concentrations and markers of obesity in patients with functional gastrointestinal disorders – Clive H. Wilder-Smith, United European Gastroenterology Journal

The Intersection Between Colonization Resistance, Antimicrobial Stewardship, and Clostridium difficile – Rossana Rosa, Current Infectious Disease Reports

Celiac Disease and Fecal Microbiota Transplantation: A New Beginning? – Shmuel Golfeyz MD, Correspondence

Gut microbiota metabolites, amino acid metabolites and improvements in insulin sensitivity and glucose metabolism: the POUNDS Lost trial – Yoriko Heianza, Nutrition

Cutting the Gordian Knot of the Microbiota – Kimberly S.Vasquez, Molecular Cell

Host: Microbiome co-metabolic processing of dietary polyphenols – An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects – Kajetan Trost, Food Research International

Clinical trials of kimchi intakes on the regulation of metabolic parameters and colon health in healthy Korean young adults – Hee-Young Kim, Journal of Functional Foods

Animal experiments

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang, Molecular Nutrition and Food Research

Effect of direct-fed microbials on culturable gut microbiotas in broiler chickens: a meta-analysis of controlled trials – Chhaiden Heak, Asian-Australasian Journal of Animal Sciences

A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome – Asha Jaja-Chimedza, Journal of Functional Foods

The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells – Alexi A. Schoenborn, Gut Microbes

Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter – Umer Zeeshan Ijaz, bioRxiv

Microbial quantity impacts Drosophila nutrition, development, and lifespan – Erin S. Keebaugh, iScience

Absence of Gut Microbiota Reduces Emotional Reactivity in Japanese Quails (Coturnix japonica) – Narjis Kraimi, Frontiers in Physiology

Animal microbiome

Identification of circular single-stranded DNA viruses in faecal samples of Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus) inhabiting the Colorado San Juan Mountains – Simona Kraberger, Infection, Genetics and Evolution

Diverse novel resident Wolbachia strains in Culicine mosquitoes from Madagascar – Claire L Jeffries, bioRxiv

Sample treatment optimization for fish stool metabolomics – Takeshi Hano, Journal of Chromatography B

Plant, root, and soil microbiome

Two decades of altered snow cover does not affect soil microbial ability to catabolize carbon compounds in an oceanic alpine heath – E.R. Jasper Wubs, Soil Biology and Biochemistry

Grazing and resource availability control soil nematode body size and abundance‐mass relationship in semi‐arid grassland – W. S. Andriuzzi, Journal of Animal Ecology

Isolation and screening of antibiotic producing actinomycetes from rhizosphere and agricultural soils – Atsede Muleta, African Journal of Biotechnology

Responses of Bougainvillea spectabilis to elevated atmospheric CO2 under galaxolide (HHCB) pollution and the mechanisms of its rhizosphere metabolism – Minzhe Zhang, Journal of Soils and Sediments

Differential effect of the nitrogen form on the leaf gas exchange, amino acid composition, and antioxidant response of sweet pepper at elevated CO2 – María C. Piñero, Plant Growth Regulation

Viral metagenomics analysis and eight novel viral genomes identified from the Dushanzi mud volcanic soil in Xinjiang, China – Dan-Ting Yu, Journal of Soils and Sediments

Efficacy of Bacillus subtilis native strains for biocontrol of Phytophthora crown and root rot of pistachio in Iran – Mohammad Moradi, Tropical Plant Pathology

Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants – Allison M. Veach, Plant and Soil

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China – Hao Guan, Bioresource Technology

Cultivated methanotrophs associated with rhizospheres of traditional rice landraces from Western India belong to Methylocaldum and Methylocystis – Monali C. Rahalkar, 3 Biotech

Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil – Xiao-Han Wang, Environmental Pollution

Enhanced removal of nitrate in the maize rhizosphere by plant growth-promoting Bacillus megaterium NCT-2, and its colonization pattern in response to nitrate – Shaohua Chu, Chemosphere

Bioactive luteoloside produced by Myroides odoratimimus, solvent-tolerant bacterium form the rhizosphere of Lonicera japonica –  Y. X. Zhao, Natural Product Research

Potential application of selected metal resistant phosphate solubilizing bacteria isolated from the gut of earthworm (Metaphire posthuma) in plant growth promotion – Jayanta  Kumar Biswas, Geoderma

Effects of Pseudomonas chenduensis and biochar on cadmium availability and microbial community in the paddy soil – Lingjuan Li, Science of The Total Environment

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Analysis on metabolic functions of stored rice microbial communities by BIOLOG ECO microplates – Zhiwen Ge, Frontiers in Microbiology

Effects of discrete bioactive microbial volatiles on plants and fungi – Birgit Piechulla, Plant, Cell, and Environment

Phylogenetic-scale disparities in the soil microbial diversity–ecosystem functioning relationship – Marta Goberna, ISME

Similar soil microbial community structure across different environments after long‐term succession: evidence from volcanoes of different ages – Shangqi Xu, Journal of Basic Microbiology

Water and extremophile microbiome

Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network – Wei Huang, Microbiology Open

The distinctive microbial community improves composting efficiency in a full-scale hyperthermophilic composting plant – Zhen Yu, Bioresource Technology

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom – Ivan S. Mikhailov, Microbial Ecology

The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra – Maria Väisänen, Microbial Ecology

Characterization of phototrophic microorganisms and description of new cyanobacteria isolated from the saline-alkaline crater-lake Dziani Dzaha (Mayotte, Indian Ocean) – M. Cellamare, FEMS Microbiology Ecology

Methanogens in the Antarctic Dry Valley Permafrost – Tatiana A. Vishnivetskaya, FEMS Microbiology Ecology

Bacterial Diversity in an Alpine Debris-Free and Debris-Cover Accumulation Zone Glacier Ice, North Sikkim, India – Mingma Thundu Sherpa, Indian Journal of Microbiology

Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase – Suhyun Kim, bioRxiv

Assessing the effect of pretreatments on the structure and functionality of microbial communities for the bioconversion of microalgae to biogas – Olivia Córdova, Frontiers in Microbiology

Great Salt Lake microbiology: a historical perspective – Bonnie K. Baxter, International Microbiology

Life from the ashes: survival of dry bacterial spores after very high temperature exposure – Lynda Beladjal, Extremophiles

Microbial and geochemical controls on waste rock weathering and drainage quality – Sharon Blackmore, Science of The Total Environment

Characterization and high-throughput sequencing of a trichlorophenol-dechlorinating microbial community acclimated from sewage sludge – Jiaxiu Song, Journal of Cleaner Production

Impacts of surface-applied residues on N-cycling soil microbial communities in miscanthus and switchgrass cropping systems – Karen A. Thompson, Applied Soil Ecology

Water is a critical factor in evaluating and assessing microbial colonization and destruction of Angkor sandstone monuments – Xiaobo Liu, International Biodeterioration & Biodegradation

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass – Justus Hardegen, Bioresource Technology

Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant – Carlos Narciso-da-Rocha, Environment International

Impact of organic waste composition on life cycle energy production, global warming and Water use for treatment by anaerobic digestion followed by composting – Sara A. Pace, Resources, Conservation and Recycling

1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms – Boštjan Murovec, Journal of Environmental Management

Comparative Metagenomics Provides Insight into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia – Joany Babilonia, Frontiers in Microbiology

Assessing the abundance of fungal populations in a full-scale membrane bioreactor (MBR) treating urban wastewater by using quantitative PCR (qPCR) – P. Maza-Márquez, Journal of Environmental Management

Food microbiology

Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa – Marcel Houngbédji, Food Microbiology

Probiotics / prebiotics

Probiotics in IBD: Combining in vitro and in vivomodels for selecting strains with both anti-inflammatory potential as well as a capacity to restore the gut epithelial barrier – Mazen Zaylaa, Journal of Functional Foods

Can prebiotics assist in the management of cognition and weight gain in schizophrenia? – Amy Chia-Ching Kao, Psychoneuroendocrinology

Probiotic potentials of Lactobacillus plantarum isolated from fermented durian (Tempoyak), a Malaysian traditional condiment – Asmariah Ahmad, Food Science and Nutrition

Bioinformatics

Identifying Heritable Communities of Microbiome by Root-Unifrac and Wishart Distribution – Yunfan Tang, bioRxiv

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive – Pedro J. Torres, Bioinformatics

Techniques

Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community – Alexandra Perras, bioRxiv

Critical Assessment of Methods to Quantify Biofilm Growth and Evaluate Antibiofilm Activity of Host Defence Peptides – Evan F. Haney, Biomolecules

June 12, 2018

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Gut and General Microbiome

Screening for Nonalcoholic Fatty Liver Disease in Inflammatory Bowel Diseases: A Cohort Study Using Transient Elastography – Chiara Saroli Palumbo – Inflammatory Bowel Diseases

Review: A critical appraisal of advances in the diagnosis of diverticular disease – Antonio Tursi – Expert Review of Gastroenterology & Hepatology  

Antimicrobial-Induced Cytopenia and Bone Marrow Hypocellularity in Patients with Cirrhosis – Anupama Patil – Bone Marrow Research

Colonic Mucosal Microbiota in Colorectal Cancer: A Single-Center Metagenomic Study in Saudi Arabia – Ahmed O. Alomair – Gastroenterology Research and Practice

Connecting homocysteine and obesity through pyroptosis, gut microbiome, epigenetics, peroxisome proliferator-activator receptor γ (PPARγ) and zinc finger protein 407 (Zfp407) – Anwesha Laha – Canadian Journal of Physiology and Pharmacology

Review: Sexual dimorphism of cardiometabolic dysfunction: Gut microbiome in the play? – Tzu-Wen L. Cross – Molecular Metabolism

Individuality and convergence of the infant gut microbiota during the first year of life – Eric J. de Muinck – Nature Communications

Reconstruction of the bifidobacterial pan-secretome reveals the network of extracellular interactions between bifidobacteria and the infant gut – Gabriele Andrea Lugli – Applied and Environmental Microbiology

Commentary: Beyond Oxalobacter: the gut microbiota and kidney stone formation – Gwen Falony – Gut

Nutritional modulation of the intestinal microbiota: future opportunities for the prevention and treatment of neuroimmune and neuroinflammatory disease – Vincent C.Lombardi – The Journal of Nutritional Biochemistry

 

Reproductive and Urinary Tract Microbiome

Review: Implantation failure of endometrial origin: what is new? –  Jose Bellver – Current Opinion in Obstetrics and Gynecology

Detecting viral genomes in the female urinary microbiome – Andrea Garretto – Journal of General Virology

Commentary: Regional Caesarean Delivery Practices, the Maternal-Infant Microbiome, and Risk for Asthma – Rebecca Entz – Journal of Obstetrics and Gynaecology Canada

 

Skin Microbiome

Insights into the skin microbiome dynamics of leprosy patients during multi-drug therapy and in healthy individuals from Brazil – Paulo E. S. Silva – Scientific Reports

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood – Scientific Reports

 

Oral and Respiratory Microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise Tornavoide Castro – Archives of Oral Biology

Bacterial biogeography of adult airways in atopic asthma – Juliana Durack – Microbiome

Review: Adenotonsillar microbiome: an update – James Jordan Johnston – Postgraduate Medical Journal

 

Animal Microbiome

The canine gut microbiome is associated with higher risk of gastric dilatation-volvulus and high risk genetic variants of the immune system – Meredith A. J. Hullar – PLOS ONE

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang – Molecular Nutrition & Food Research

Deficiency of BrpA in Streptococcus mutans Reduces Virulence in Rat Caries Model – Zezhang T. Wen – Molecular Oral Microbiology

Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure – Xue-Ying Zhang – Microbiome

Abnormal gut microbiota composition contributes to cognitive dysfunction in SAMP8 mice – Gaofeng Zhan – Aging

The role of regulator FucP in Edwardsiella tarda pathogenesis and the inflammatory cytokine response in tilapia – Jiayan Wu – Fish & Shellfish Immunology

Malassezia pachydermatis from animals: Planktonic and biofilm antifungal susceptibility and its virulence arsenal – Raimunda Sâmia Nogueira Brilhante – Veterinary Microbiology

 

Beneficial Microbes

Oral administration of Bifidobacterium bifidum TMC3115 to neonatal mice may alleviate IgE-mediated allergic risk in adulthood – R.Y. Cheng – Beneficial Microbes

Three-Month Feeding Integration With Bifidobacterium Strains Prevents Gastrointestinal Symptoms in Healthy Newborns – Irene Aloisio – Frontiers in Nutrition

 

Bioinformatics and Genomics

Review: Interrogating the microbiome: experimental and computational considerations in support of study reproducibility – Carine Poussin – Drug Discovery Today

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software – Toby J. Wilkinson – Frontiers in Microbiology

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity – Andrea Hahn – Frontiers in Microbiology

Next-Generation Machine Learning for Biological Networks – Diogo M. Camacho – Cell

 

June 8, 2018

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A short Digest today with primarily preprints. A policy piece on diabetic patient care in the UK, Wolbachia strains never found before in Anopheles mosquitoes, and fecal pollution contributing to antibiotic resistant genes in waste water.

Jobs

Postdoctoral Fellowship in Microbiome Data Science – Johns Hopkins University

General microbiology

Preprint: DivIVA concentrates mycobacterial cell envelope assembly for initiation and stabilization of polar growth – Emily Sarah Melzer et al. – bioRxiv

Preprint: Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA – David G Welkie et al. – bioRxiv

Preprint: The fungal-specific Hda2 and Hda3 proteins regulate morphological switches in the human fungal pathogen Candida albicans – Misty Peterson et al. – bioRxiv

Preprint: Chance and pleiotropy dominate genetic diversity in complex bacterial environments – Lianet Noda-Garcia et al. – bioRxiv

Preprint: Molecular basis for the evolution of species-specific hemoglobin capture by pathogenic Staphylococcus – Jacob E Choby et al. – bioRxiv

Antibiotic resistance

Preprint: Comparison of trimethoprim-sulfamethoxazole versus ciprofloxacin monotherapy in Stenotrophomonas maltophilia bloodstream infections in children – Ahu Aksay et al. – bioRxiv

Preprint: The reduced prevalence of macrolide resistance in Mycoplasma pneumoniae clinical isolates from pediatric patients in Beijing in 2016 – Xiu jun Tian et al. – bioRxiv

Preprint: The key lethal effect existed in the antibacterial behavior of short, medium, and long chain fatty acid monoglycerides on Escherichia coli – Song Zhang et al. – bioRxiv

Human oral microbiome

Preprint: The stress hormone cortisol induces virulence in the oral microbiome – Ana Emilia Duran-Pinedo et al. – bioRxiv

Human gut microbiome

** Policy: Diabetes UK nutrition guidelines: reinforcing the foundations of diabetes care – Mark Greener – Practical Diabetes

Animal microbiome

** Preprint: Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa – Claire L Jeffries et al. – bioRxiv

Plant, root and soil microbiome

Preprint: The effect of susceptible and resistant potato cultivars on bacterial communities in the tuberosphere of potato in soil suppressive or conducive to common scab disease – Marketa Sagova-Mareckova et al. – bioRxiv

Preprint: Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit – Peter McAtee et al. – bioRxiv

Water and extremophile microbiome

** Preprint: Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments – Antti Karkman et al. – bioRxiv

Phages and viruses

Preprint: Adomaviruses: an emerging virus family provides insights into DNA virus evolution – Nicole L Welch et al. – bioRxiv

Preprint: Epstein-Barr Virus May Contribute to Central Nervous System Involvement in HIV-positive Individuals – Tommaso Lupia et al. – bioRxiv

Bioinformatics

Preprint: PorSignDB: a database of in vivo perturbation signatures for dissecting clinical outcome of PCV2 infection – Nicolaas Van Renne et al. – bioRxiv

 

June 7, 2018

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Today’s microbiology highlights: Microbiome in pregnancies, microbiome of SLE, Mycobacteria of a karst region, skin microbiome of non-human mammals. And lab diversity, potential problem in big data, Paris climate agreement of 1.5⁰C increase among the non-microbe highlights.

 

General microbiome

Biochemical, molecular and antibiotic resistance profile of multi-potential toluene metabolizing bacteria isolated from tannery effluents – F Muccee – bioRxiv

Pregnancy and early life

Review: Microbiome in normal and pathological pregnancies: A literature overview – CR Taddei – AJRI

Multi-site human microbiome

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells – AP Chan – Scientific Reports

 

Human gut microbiome

Proton Pump Inhibitor Initiation and Withdrawal affects Gut Microbiota and Readmission Risk in Cirrhosis – JS Bajaj – AJG

Review: Early-Life Food Nutrition, Microbiota Maturation and Immune Development Shape Life-Long Health – X Zhou – Critical Reviews in Food Science and Nutrition

Animal experiments

Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota – F Cignarella – Cell Metabolism

The Microbiome and Systemic Lupus Erythematosus – JT Rosenbaum – The New England Journal of Medicine

Review: The probiotic effectiveness in experimental colitis is correlated with gut microbiome and host genetic features – S Suwal – bioRxiv

Animal microbiome 

Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia – AA Ross – PNAS

Alterations in the gut (Gallus gallus) microbiota following the consumption of zinc biofortified wheat (Triticum aestivum) -based diet – S Reed – ACS

Water and extremophile microbiome 

Nontuberculous mycobacteria in the environment of Hranice Abyss, the world’s deepest flooded cave (Hranice karst, Czech Republic) – I Pavlik – Environmental Science and Pollution Research

Built environment 

Toxicity assessment of pharmaceutical compounds on mixed culture from activated sludge using respirometric technique: The role of microbial community structure – IA Vasiliadou – Science of The Total Environment

Food microbiology

Effect of herbal feed additives on performance parameters, intestinal microbiota, intestinal morphology and meat lipid oxidation of broiler chickens – I Giannenas – British Poultry Science

 

Techniques

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research – PD Schloss – mBio

Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens – L Guo – bioRxiv

Microbes in the news

Media Advisory: Live exhibit of dance and song on tiny world of bacteria inside us comes to Buffalo Museum of Science – UB News Center

Non-microbiology picks

These labs are remarkably diverse — here’s why they’re winning at science – Nature

Big data little help in megafauna mysteries – Nature

What does it take to make an institution more diverse? – Nature

The many possible climates from the Paris Agreement’s aim of 1.5 °C warming – Nature

 

June 6, 2018

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Today’s highlights: Microbes on aging flue-cured tobaccos, impact of gut microbes on neurological disease, gut microbiome of non-human microbiome, diet simplification selects for high gut microbial diversity.

General microbiome

Species Diversity and Functional Prediction of Surface Bacterial Communities on Aging Flue-Cured Tobaccos – F Wang – Current Microbiology

Oxygen restriction induces a viable but non-culturable population in bacteria – LA Kvich – bioRxiv

Human respiratory microbiome

Airway Microbiota Is Associated with Up-Regulation of the PI3K Pathway in Lung Cancer – J-C J Tsay – American Journal of Respiratory and Critical Care Medicine

Human skin microbiome

Role of anaerobes in polymicrobial communities and biofilms complicating diabetic foot ulcers – SL Percival – International Wound Journal

Human gut microbiome

Impact of gut microbiota on neurological diseases: Diet composition and novel treatments – A L-Garcia – Critical Reviews in Food Science and Nutrition

Composition and richness of the serum microbiome differ by age and link to systemic inflammation – TW Buford – GeroScience

Animal microbiome 

Review: The gut microbiome of nonhuman primates: Lessons in ecology and evolution – JB Clayton – American Journal of Primatology

Culture-based analysis of Pristionchus-associated microbiota from beetles and figs for studying nematode-bacterial interactions – N Akduman – PLoS One

Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas – H Li – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Rhizospheric bacterial isolates of grass pea (Lathyrus sativus L.) endowed with multiple plant growth promoting traits – A Mussa – Journal of Applied Microbiology

Diversity of culturable methylotrophic bacteria in different genotypes of groundnut and their potential for plant growth promotion – R. Krishnamoorthy – 3 Biotech

Environmental factors shaping the diversity of bacterial communities that promote rice production – Z Wu – BMC Microbiology

Water and extremophile microbiome 

Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay – MS Reza – Gene

Decay of sewage-associated bacterial communities in fresh and marine environmental waters and sediment – W Ahmed – Applied Microbiology and Biotechnology

 

June 5, 2018

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A model to study the effect of horizontal gene transfer on maintaining equilibrium in microbial communities, antimicrobial tolerance in brewery biofilms, the sperm whale microbiota.

General microbiome

Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities – Yuhang Fan – Journal of Theoretical Biology

Human gut microbiome

Review: Carcinogenesis as a Result of Multiple Inflammatory and Oxidative Hits: a Comprehensive Review from Tumor Microenvironment to Gut Microbiota – Floriana Morgillo – Neoplasia

Animal experiments

Extrathymically Generated Regulatory T Cells Establish a Niche for Intestinal Border-Dwelling Bacteria and Affect Physiologic Metabolite Balance – Clarissa Campbell – Immunity

Animal microbiome

Pre-print: Microbiome interaction networks and community structure from lab-reared and field-collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus mosquito vectors – Shivanand Hegde – bioRxiv

Pre-print: Metagenomics reveals diet-specific specialization in fungus gardens of grass- and dicot-cutter ants – Lily Khadempour – bioRxiv

Occurrence of anthropozoonotic parasitic infections and faecal microbes in free-ranging sperm whales (Physeter macrocephalus) from the Mediterranean Sea – Carlos Hermosilla – Parasitology Research

Plant, root, and soil microbiome

Root-associated bacteria influencing mycelial growth of Tricholoma matsutake (pine mushroom) – Seung-Yoon Oh – Journal of Microbiology

Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area – Katie M McGee – Microbial Ecology

Water and extremophile microbiome

Pre-print: Competition and Synergy Between Prochlorococcus and Synechococcus Under Ocean Acidification Conditions – James Jeffrey Morris – bioRxiv

Quantifying the Relative Contributions of Environmental Sources to the Microbial Community in an Urban Stream under Dry and Wet Weather Conditions – Darshan Baral – Applied and Environmental Microbiology

The deep continental subsurface: the dark biosphere – Cristina Escudero – International Microbiology

Food microbiology

Competitive inter-species interactions underlie the increased antimicrobial tolerance in multispecies brewery biofilms – Ilse Parijs – ISME Journal

Phages and viruses

Influence of gut microbiome on mucosal immune activation and SHIV viral transmission in naive macaques – Yongjun Sui – Mucosal Immunity

Techniques

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

June 3, 2018

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Today’s digest full of great and fun studies including a fungal survey of the atmosphere and links between gut microbiome and MS.

General Microbiome

RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Egert M. Methods

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.Cardona C. mSystems

Biohydrogen production from space crew’s waste simulants using thermophilic consolidated bioprocessing.Wang J. Bioresource Technology

Prevalence of <i>Trichomonas vaginalis</i> infection and protozoan load in South African women: a cross-sectional study.de Waaij DJ.BMJ Open

Time course metabolome of Roux-en-Y gastric bypass confirms correlation between leptin, body weight and the microbiome.Seridi L. PLoS One

Gut Microbiome

A gut feeling about multiple sclerosis.Quintana FJ. Proceedings of the National Academy of Sciences

Dietary fat and gut microbiota: mechanisms involved in obesity control.Coelho OGL. Critical Reviews in Food Science and Nutrition

Probiotic Species in the Modulation of Gut Microbiota: An Overview.Azad MAK J. Biomedical Research International.

The Relationship between Frequently Used Glucose-Lowering Agents and Gut Microbiota in Type 2 Diabetes Mellitus.Lv Y. Journal of Diabetes Research

The Gut Microbiome Profile in Obesity: A Systematic Review.Castaner O. International Journal of Endocrinology.

The <i>Lactobacillus</i> Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation.O’Flaherty S. mSphere

Skin Microbiome

Early-life skin microbiota in hospitalized preterm and full-term infants.Younge NE. Microbiome.

Oral Microbiome

Stimulated and unstimulated saliva samples have significantly different bacterial profiles.Gomar-Vercher S. PLoS

Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status.Presti RM. AIDS

Oral microbiota in youth with perinatally acquired HIV infection. Starr JR. Microbiome

Air and Water Microbiome

Biogeochemical probing of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland.Cousins CR. Geobiology

Taxonomic diversity of fungi deposited from the atmosphere.Woo C. ISME Journal.

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.Garcia SL. mSphere.

Animal Experiments and Microbiome

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates.Zhang Z. Microbiome

Longevity extension in Drosophila through gut-brain communication.Westfall S. Scientific Reports

Exploring the diversity-stability paradigm using sponge microbial communities.Glasl B. Scientific Reports

Exploring the Microbiome of Callinectes sapidus (Maryland Blue Crab).Ramachandran P. Genome Announcements

Effect of different types of olive oil pomace dietary supplementation on the rumen microbial community profile in Comisana ewes.Mannelli F. Scientific Reports

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period.Salem SE. Scientific Reports

Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus).Mekuchi M. PLoS One

Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors.Herstad KMV.PLoS One

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera). Ziganshina EE. Biomedical Research International.

Plant and Soil Microbiomes

Antibiotic Resistance in Plant-Pathogenic Bacteria. Sundin GW. Annual Review of Phytopathology

Characterization of Microbial Communities in Pilot-Scale Constructed Wetlands with <i>Salicornia</i> for Treatment of Marine Aquaculture Effluents.Ma X. Archaea.

Fall Armyworm-Associated Gut Bacteria Modulate Plant Defense Responses.Acevedo FE. Molecular Plant-Microbe Interactions

Multifunctional potential of endophytic and rhizospheric microbial isolates associated with Butia purpurascens roots for promoting plant growth.da Silva CF. Antonie Van Leeuwenhoek

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.Gołębiewski M. Microbial Ecology

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana.Bartoli C. ISME Journal.