Category Archives: Animal microbiome

December 6, 2019

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Today’s post is about metabolic networks of the human gut microbiota with host, how aging affects microbial world in humans, microbiome in honey bee and lifestyle dependent gut microbiota gradients in diverse Indian population. Have a nice weekend!

General microbiome

Review: Metabolic networks of the human gut microbiota – Susannah Selber-Hnatiw – Microbiology

Review: Cannabinoids and the Microbiota‐Gut‐Brain‐Axis: Emerging Effects of Cannabidiol and Potential Applications to Alcohol Use Disorders – Hollis C. Karoly – Alcoholism Clinical and Experimental Research

Review: The Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging – Oscar Salvador Barrera-Vázquez – Journal of Gerontology

Review: Nanotechnology intervention of the microbiome for cancer therapy – Wantong Song – Nature Nanotechnology

Commentary: Gut microbiome influences exercise response – Claire Greenhill – Nature Reviews Endocrinology

Human microbiome

Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma – Victor Tetz – Scientific Reports

Lifestyle induced microbial gradients: An Indian perspective – Rashmi Singh – Frontiers in Microbiology

Microbiota, type 2 diabetes and non-alcoholic fatty liver disease: protocol of an observational study – Benedetta M. Motta – Journal of Translational Medicine

Antibiotic exposure and the risk of colorectal adenoma and carcinoma: systematic review and meta‐analysis of observational studies – Leigh N. Sanyaolu – Colorectal Disease

Higher frequency of vertebrate‐infecting viruses in the gut of infants born to mothers with type 1 diabetes – Ki Wook Kim – Pediatric Diabetes

Animal experiments

Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics – Jie Han – Scientific Reports

Division of labor in honey bee gut microbiota for plant polysaccharide digestion – Hao Zheng – PNAS

The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera) – Michelle A. Taylor – PlosOne

Seven-day Green Tea Supplementation Revamps Gut Microbiome and Caecum/Skin Metabolome in Mice from Stress – Eun Sung Jung – Scientific Reports

Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonization travel – Raies A. Mir – PlosOne

Characterization of the cecal microbiome composition of Wenchang chickens before and after fattening – Zhen Tan – PlosOne

SOD1 deficiency alters gastrointestinal microbiota and metabolites in mice – Haruka Sagi – Experimental Gerontology

Plant, soil, root microbiome

Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere – Michael D. Jochum – PlosOne

Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing – Preshita S. Gadkari – FEMS Microbiology Ecology

Techniques

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces – Richard W. Hagan – American Journal of Physical Anthropology

Microbes in the news

How Microbiomes Affect Fear – Quanta Magazine

Rainforest Dwellers and Urbanites Have Consistently Different Microbiomes – Scientific American

Human Microbiome Modulators Market is Furbishing worldwide with Bayer, BioGaia, Chr. Hansen Holding, DowDuPont – News Description

December 4, 2019

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Highlights: Microbiome of human milk, AMON to integrate microbiome and metabolome data, soil microbiomes, skin microbiome based news and many more!

General microbiome

The fight for glycans in reproductive tract microbial ecology – MIH Pishchany – AJOG

Microbiota, a Third Player in the Host–Plasmodium Affair – D Mukherjee – Trends in Parasitology

Pregnancy and early life

Baby’s First Microbes: The Microbiome of Human Milk – MC Collado – How Fermented Foods Feed a Healthy Gut Microbiota

Human respiratory microbiome

Anterior Nares Diversity and Pathobionts Represent Sinus Microbiome in Chronic Rhinosinusitis – ID Boeck – mSphere

Animal microbiome 

Next generation sequencing reveals significant variations in bacterial compositions across the gastrointestinal tracts of the Indian major carps, rohu (Labeo rohita), catla (Catla catla) and mrigal (Cirrhinus cirrhosis) – MJ Foysal – Letters in Applied Microbiology

Plant, root, and soil microbiome

Rewetting of three drained peatlands drives congruent compositional changes in pro- and eukaryotic microbiomes through environmental filtering – M Weil – bioRxiv

The influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation –  R Bartelme – bioRxiv

Rhizosphere: a home for human pathogens – R Sharma – Plant Biotic Interactions

Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes – SD Mandal – Environmental Monitoring and Assessment

Soil bacterial and fungal communities exhibit distinct long-term responses to disturbance in temperate forests – ED Osburn – Frontiers in Microbiology

Decomposition of mixtures of cover crop residues increases microbial functional diversity – SM Drost – Geoderma

Techniques

AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data – M Shaffer – BMC Bioinformatics

Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity – GS Watts – PLoS Computational Biology

Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes – BO Oyserman – bioRxiv

Microbes in the news

Korean beauty makers join the rush towards new skin gold mine of microbiome – Pulse

Mode of Delivery May Alter Microbiome, But Study Finds No Link to Later GI Issues – Gastro Endo News

Smart Skin care – Cosmetics Design Europe

The Dynamic Microbiome – Gen Eng News

microRNA Found in Gut Microbiome May Unlock Future Therapeutic Approach for MS – Multiple Sclerosis News Today

A Matchmaker for Microbiomes – Identifying Relationships of Microbes and Metabolites – Scitech Daily

November 23, 2019

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In today’s digest read about the Darobactin (a new antibiotic that selectively kills Gram-negative pathogens by binding to the BamA protein, located in the external membrane of Gram-negative bacteria), temporal stability of the rumen microbiota, and Gardnerella species (Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis) in the vaginal microbiome. And, check out 2019 Holiday Gift Guide For Microbe Lovers. Happy weekend!

General microbiome

*A new antibiotic selectively kills Gram-negative pathogens – Yu Imai – Nature

Read the story behind the paper by Roberto Molar Candanosa, Northeastern University.

Gut microbiome

Review: The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health – Jillian L. Waters & Ruth E. Ley – BMC Biology

The gut microbiota influences how circulating immune cells in humans change from one day to the next – Jonas Schluter – bioRxiv

Vaginal microbiome

*Resolution and Cooccurrence Patterns of Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis within the Vaginal Microbiome – Janet E. Hill – Infection and Immunity

Clinical validation of the Aptima Bacterial Vaginosis and Aptima Candida/Trichomonas Vaginitis Assays: results from a prospective multi-center clinical study – Jane R. Schwebke – Journal of Clinical Microbiology

Review: Understanding and interpreting community sequencing measurements of the vaginal microbiome – HL Berman – BJOG : an International Journal of Obstetrics and Gynaecology

Endocervical microbiome

Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia – Heng Choon Cheong – PlosOne

Uterine microbiome

Does dysbiotic endometrium affect blastocyst implantation in IVF patients? – Tomoko Hashimoto & Koichi Kyono – Journal of Assisted Reproduction and Genetics

Oral microbiome

Oral microbial community composition is associated with pancreatic cancer: A case‐control study in Iran – Emily Vogtmann – Cancer Medicine

Animal microbiome

*Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements – Timothy J. Snelling – Animal Microbiome

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens – Laura Glendinning – Animal Microbiome

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status – Tucker Andrews – PlosOne

Inulin improves the egg production performance and affects the cecum microbiota of laying hens – Hongmei Shang – International Journal of Biological Macromolecules

Animal experiments

Effects of Debaryomyces hansenii treatment on intestinal mucosa microecology in mice with antibiotic-associated diarrhea – Ao Zeng – PlosOne

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium – Andre Mu – bioRxiv

Hepatitis B Virus Infection Alters Gut Microbiota Composition in Mice – Qingfeng Zhu – Front. Cell. Infect. Microbiol.

Human Gut Microbiome Transplantation in Ileitis Prone Mice: A Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients – Abigail R Basson – Inflammatory Bowel Diseases

Effects of an Escherichia coli exopolysaccharide on human and mouse gut microbiota in vitro – Baiyuan Li – International Journal of Biological Macromolecules

Ion Transport Basis of Diarrhea in a Mouse Model of Adoptive T Cell Transfer Colitis – Dulari Jayawarden – Digestive Diseases and Sciences

Water microbiome

Rewetting of three drained peatlands drives congruent compositional changes in pro- and eukaryotic microbiomes through environmental filtering – Micha Weil – bioRxiv

Phages and viruses

Herpes Simplex Virus Infection, Acyclovir and IVIG Treatment All Independently Cause Gut Dysbiosis – Chandran Ramakrishna – bioRxiv

Svetlana’s pick

Gift guide for this holiday season!
by Justine Dees

November 11, 2019

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Monday’s morning digest is all about interesting updates in microbiome field – real time sampling of international travelers to study antibiotic resistant bacteria, new techniques on using rectal swabs instead of fecal samples to study infant microbiota, 16srRNA gene sequencing for strain level identification and if neutraceutical consumption helps in multiple sclerosis! Finally some interesting review articles on microbial ecology in wine making and a Movember month featured article on association of gut microbiome with men’s sexual health. Enjoy reading!

General microbiome

From the vineyard to the winery: how microbial ecology drives regional distinctiveness of wine – Di Liu – Frontiers in Microbiology

The Gut Microbiome and Men’s Sexual Health – Mohamad M. Osman – Current Sexual Heath Reports

Antibacterial Soaps and Other Cleaners May Actually Be Aiding in the Development of Super Bacteria – Shimon Shatzmiller – Pharmacology, Toxicology and Pharmaceutics

Dietary lipids, gut microbiota and lipid metabolism – Marc Schoeler – Reviews in Endocrine and Metabolic Disorders

Human microbiome

Functional characterisation of gut microbiota and metabolism in Type 2 diabetes indicates that Clostridiales and Enterococcus could play a key role in the disease – Marina Mora-Ortiz – BioRxiv

Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions – A. Kantele – BioRxiv

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome – Zhuye Jie – BioRxiv

Antimicrobial resistance gene prevalence in a population of patients with advanced dementia is related to specific pathobionts – Aislinn D. Rowan-Nash – BioRxiv

Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018 – Mónica Arteaga – BioRxiv

Molecular Reconstruction of the Diet in Human Stool Samples – Frank Maixner – mSystems

Infant microbiome

Impacts of Delivery Mode on Very Low Birth Weight Infants’ Oral Microbiome – Hongping Li – Pediatrics and Neonatology

Biomarker Research in ADHD: the Impact of Nutrition (BRAIN) – study protocol of an open-label trial to investigate the mechanisms underlying the effects of a few-foods diet on ADHD symptoms in children – Tim Stobernack – BMJ Open

Immunometabolic approaches to prevent, detect, and treat neonatal sepsis – Maria Giulia Conti – Pediatric Research

Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing – Marta Reyman – Scientific Reports

Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course – R. E. Ventura – Scientific Reports

Animal experiments

Vasoactive intestinal peptide deficiency is associated with altered gut microbiota communities in male and female C57BL/6 mice – Manpreet Bains – Frontiers in Microbiology

Metabolic analysis of regionally distinct gut microbial communities using an in vitro platform – Jenni Firrman – Agricultural and Environmental Chemistry

Effect of Diet on the Enteric Microbiome of the Wood-Eating Catfish Panaque nigrolineatus – Harold J. Schreier – Frontiers in Microbiology

A high-fat/high-protein, Atkins-type diet exacerbates Clostridioides (Clostridium) difficile infection in mice, whereas a high-carbohydrate diet protects – Chrisabelle C. Mefferd – BioRxiv

Plant, soil, root microbiome

Effects of repeated applications of urea with DMPP on ammonia oxidizers, denitrifiers, and non-targeted microbial communities of an agricultural soil in Queensland, Australia – Aineah Obed Luchibia – Applied Soil Ecology

Covariation of diet and gut microbiome in African megafauna – Tyler R. Kartzinel – PNAS

Fungal communities resist recovery in sand mine restoration – Miranda Hart – Frontiers in Forest and Global Change

Microbial community structure and ecology in sediments of a pristine mangrove forest – C.O.Santana – BioRxiv

Bridging the gap between single-strain and community-level plant-microbe chemical interactions – Bridget O’Banion – Molecular Plant-Microbe Interactions

A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome – Johan HJ Leveau – Current Opinion in Microbiology

Water microbiome

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems – Amy E. Zimmerman – Nature Reviews Microbiology

Down to the bone: the role of overlooked endolithic microbiomes in reef coral health – Mathieu Pernice – ISME Journal

Differential responses of stream water and bed sediment microbial communities to watershed degradation – Hehuan Liao – Environment International

B12 production by marine microbial communities and Dinoroseobacter shibae continuous cultures under different growth and respiration rates – Josue Villegas-Mendoza – Aquatic Microbial Ecology

Quantifying the contribution of microbial immigration in engineered water systems – Ran Mei – Microbiome

Microbial community rearrangements in power-to-biomethane reactors employing mesophilic biogas digestate – Norbert Ács – Frontiers in Energy Research

Techniques

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis – Jethro S. Johnson – Nature Communications

AMR – An R Package for Working with Antimicrobial Resistance Data – Matthijs S. Berends – BioRxiv

Probiotics Prebiotics

The effect of emerging nutraceutical interventions for clinical and biological outcomes in multiple sclerosis: A systematic review – Wolfgang Marx – Multiple Sclerosis and Related Disorders

Resveratrol treatment improves the altered metabolism and related dysbiosis of gut programed by prenatal high-fat diet and postnatal high-fat diet exposure – Yi-Chuan Huang – The Journal of Nutritional Biochemistry

The effects of inulin on gut microbial composition: a systematic review of evidence from human studies – Quentin Le Bastard – European Journal of Clinical Microbiology & Infectious Diseases

November 8, 2019

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Today’s week-end digest is about new bioinformatic tools (MGnify, PIME, MDiNE) for microbiota analysis, how chemical and built environment of home affects human microbiota and  guidelines for the gut microbiome studies in hypertension.

General microbiome

Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners – Sara C. Di Rienzi – Advances in Nutrition

Bacteriophages in gastroenterology—from biology to clinical applications – João Sabino – Alimentary Pharmacology and Therapeutics

Boosting natural history research via metagenomic clean-up of crowdsourced feces – Amrita Srivathsan – Plos Biology

Human microbiome

Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis – Stuart Astbury – Gut Microbes

Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension – Francine Z. Marques – Hypertension

The association between dietary fibre deficiency and high-income lifestyle-associated diseases: Burkitt’s hypothesis revisited – Stephen J. O’Keefe – The Lancet Gastroenterology and Hepatology

Animal experiments

Bacterial Swarming as a Protective Response to Intestinal Stress – Weijie Chen – BioRxiv

Flaxseed oil supplementation improves intestinal function and immunity, associated with altered intestinal microbiome and fatty acid profile in pigs with intrauterine growth retardation – Lianqiang Che – Food and Function

Gamma-aminobutyric acid-producing lactobacilli positively affect metabolism and depressive-like behaviour in a mouse model of metabolic syndrome – E. Patterson – Scientific Reports

Plant, root and soil microbiome

Short term effects of different green manure amendments on the composition of main microbial groups and microbial activity of a submerged rice cropping system – Muhammad Israr Khan – Applied Soil Ecology

Cost-effective in-situ remediation technologies for complete mineralization of dyes contaminated soils – Vipul R. Patel – Chemosphere

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea – Lijun Bao – Microorganisms

Tracing the evolutionary routes of plant–microbiota interactions – Carmen Escudero-Martinez – Current Opinion in Microbiology

Water microbiome

Diet shapes cold‐water corals bacterial communities – Pierre E. Galand – Environmental Microbiology

Built Environment

Home chemical and microbial transitions across urbanization – Laura-Isobel McCall – Nature Microbiology

Techniques

Learning representations of microbe–metabolite interactions – James T. Morton – Nature Methods

MGnify: the microbiome analysis resource in 2020 – Alex L. Mitchell – Nucleic Acids Research

PIME: A package for discovery of novel differences among microbial communities – Luiz Fernando W. Roesch – Molecular Ecology Resources

MDiNE: A model to estimate differential co-occurrence networks in microbiome studies – Kevin McGregor – Bioinformatics

Probiotics

Fermentation of plant-based milk alternatives for improved flavour and nutritional value – Muzi Tangyu – Applied Microbiology and Biotechnology

Modulations of Probiotics on Gut Microbiota in a 5‐Fluorouracil‐Induced Mouse Model of Mucositis – Chun Yan Yeung – Journal of Gastroenterology and Hepatology

The effect of an additive containing three Lactobacillus species on the fermentation pattern and microbiological status of silage – Maja Fijałkowska – Journal of the Science of Food and Agriculture

Microbes in the news

Gut Microbiome Puts the Brakes on Iron Absorption – Michigan Medicine

The Link Between Sleep and Your Gut Microbiome – Health central

Microbiome in China: Cosmetic trend will ‘heat up’ by the end of 2020, says expert – Cosmetics Design-Asia

Enterome Enters Research Collaboration With Major Cancer Center Focused on New Microbiome-derived Immunotherapies – Yahoo Finance

Non Microbiology Picks

Is running associated with a lower risk of all-cause, cardiovascular and cancer mortality, and is the more the better? A systematic review and meta-analysis – Zeljko Pedisic – British Journal of Sports Medicine

October 28, 2019

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Monday morning digest is about microbiome and microbial metabolites in depression, neuronal function and fear extinction, and epilepsy in children; functional foods in lung cancer risk and microbiota based novel marker of colorectal cancer.

General microbiome

Gut microbial metabolites in depression: understanding the biochemical mechanisms – Giorgia Caspani – Microbial Cell

Engineering commensal bacteria to rewire host–microbiome interactions – In Young Hwang – Current Opinion in Biotechnology

Human microbiome

The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study – Josef Wagner – Microbiome

Autoinducer-2 of gut microbiota, a potential novel marker for human colorectal cancer, is associated with the activation of TNFSF9 signaling in macrophages – Qing Li – Oncoimmunology

Distinct Gut Microbiota Composition and Functional Category in Children With Cerebral Palsy and Epilepsy – Congfu Huang – Frontiers in Pediatrics

Drug resistant gut bacteria mimic a host mechanism for anticancer drug clearance – Peter Spanogiannopoulos – BioRxiv

A comprehensive human minimal gut metagenome extends the host’s metabolic potential – Marcos Parras-Molto – BioRxiv

Enriched taxa were found among the gut microbiota of centenarians in East China – Na Wang – PlosOne

Animal experiments

The microbiota regulate neuronal function and fear extinction learning – Coco Chu – Nature

Syntrophic growth of alkaliphilic anaerobes controlled by ferric and ferrous minerals transformation coupled to acetogenesis – Daria G. Zavarzina – ISME Journal

Contribution of fungal microbiome to intestinal physiology, early-life immune development and mucosal inflammation in mice – Erik van Tilburg Bernardes – BioRxiv

Plant, root, soil microbiome

Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization – Shuaimin Chen – Microbiome

Water microbiome

Deterministic and stochastic processes driving the shift in the prokaryotic community composition in wastewater treatment plants of a coastal Chinese city – Liyuan Hou – Applied Microbiology and Biotechnology

Metabolic specializations within a bacterial community to create living rocks – Samantha C Waterworth – BioRxiv

Probiotics/Prebiotics

Association of Dietary Fiber and Yogurt Consumption With Lung Cancer Risk – Jae Jeong Yang – JAMA Oncology

Effect of probiotics on the occurrence of nutrition absorption capacities in healthy children: a randomized double-blinded placebo-controlled pilot study – A. Ballini – European Review for Medical and Pharmacological Sciences

Microbes in the news

Can we predict the future? Bill Gates says yes, in this one area – CNBC

Exposure to Sunlight Boosts Good Gut Microbiome Bacteria, and Vitamin D Levels – Genetic Engineering and Biotechnology News

Harnessing the Power of Microbes to Fight Cancer – Medscape

October 26, 2019

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Highlights: Bacterial communities in aquaculture, crocodiles, tadpoles, mushrooms, coasts, sports facilities; viruses; standardization issues of human microbiome research; some cool events and news hot off the press!

 

Events and jobs

2019 Genome Center Halloween Symposium – 31/10/2019 – UCD, USA

MB Seminar: Marine Host-Microbiome Interactions: Challenges and Opportunities (Dr. Jonathan Eisen, UC Davis) – 22/11/2019 – UCSD, USA

General microbiome 

Metabolic specializations within a bacterial community to create living rocks – Samantha C Waterworth – bioRxiv

Analysis of bacterial microbiome associated with nylon and copper nets in an aquaculture context – Paula Canada – Aquaculture

The gut-eye-lacrimal gland-microbiome axis in Sjögren Syndrome – Claudia M. Trujillo-Vargas – The Ocular Surface

Multi-site human microbiome

DNA extraction for human microbiome studies: the issue of standardization  – K. Leigh Greathouse Genome Biology

Storage media and not extraction method has the biggest impact on recovery of bacteria from the oral microbiome – Xiaoyan Zhou – Nature

Factors contributing to interindividual variation in retronasal odor perception from aroma glycosides: the role of odorant sensory detection threshold, oral microbiota and hydrolysis in saliva – Mango Parker – ACS

Animal experiments 

Contribution of fungal microbiome to intestinal physiology, early-life immune development and mucosal inflammation in mice – Erik van Tilburg Bernardes – bioRxiv

Animal microbiome 

Gut microbiota structure differs between honey bees in winter and summer – Lucie Kešnerová – bioRxiv

Characterisation of the intestinal microbiota of commercially farmed saltwater crocodiles, Crocodylus porosus – Nicky-Lee Willson – Applied Microbiology and Biotechnology

Changes in intestinal microbial community of Rana chensinensis tadpoles during metamorphosis – Hongyu Yang – Aquaculture

Plant, root, and soil microbiome

Impact of agro-farming activities on microbial diversity of acidic red soils in a Camellia Oleifera Forest – Jun Li – Revista Brasileira de Ciência do Solo

A horizon scan of priorities for coastal marine microbiome research – Stacey M. Trevathan-Tackett – Nature

Water and extremophile microbiome 

Effects of disinfection efficiency on microbial communities and corrosion processes in drinking water distribution systems simulated with actual running conditions – Ying Zhu – Journal of Environmental Sciences

Built environment 

Microbial diversity of bioaerosol inside sports facilities and antibiotic resistance of isolated Staphylococcus spp. – Marta Małecka-Adamowicz – Aerobiologia

Food microbiology

Comparing approaches for capturing bacterial assemblages 2 associated with symptomatic (bacterial blotch) and asymptomatic 3 mushroom (Agaricus bisporus) caps – Samuel J. Martins – APS

Comprehensive Understanding of the Bacterial Populations and Metabolites Profile of Fermented Feed by 16S rRNA Gene Sequencing and Liquid Chromatography–Mass Spectrometry – Wei Jin – MDPI Metabolites

Phages and viruses

Viruses RIG up intestinal immunity – Sanghyun Lee – Nature Immunology

Gut DNA Virome Diversity and Its Association with Host Bacteria Regulate Inflammatory Phenotype and Neuronal Immunotoxicity in Experimental Gulf War Illness – Ratanesh K Seth – MDPI Viruses

Viral quasispecies – Esteban Domingo – PLoS Genetics

Techniques

Effective application of machine learning to microbiome-based classification problems – Begüm D. Topçuoğlu – bioRxiv

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey – bioRxiv

Microbes in the news

Even the Fetus Has Gut Bacteria, Study Shows – News Wise

Tropical Air Microbiome Analysis Reveals Daily Cycle, Environmental Drivers – genomeweb

Global Microbiome Sequencing Market – Yahoo

How our day-to-day food intake shapes our gut microbiota – Gut microbiota for health

Tracking down the functions of the microbiome – phys.org

Unhealthy gut microbiome reduces brain synaptic pruning, impairs learning – News Medical

Harnessing the Power of Microbes to Fight Cancer – Medscape.com