June 11, 2019

Today’s digest is about microbiome and Alzheimer’s disease association, global survey of arsenic related genes in soil microbiome,  Bifidobacterium bifidus in infant gut and a preprint on selection in host microbiome evolution.

General microbiome

Understanding the Role of the Gut Microbiome and Microbial Metabolites in Obesity and Obesity-Associated Metabolic Disorders: Current Evidence and Perspectives – Natalia Vallianou – Current Obesity Reports

Alzheimer’s disease and symbiotic microbiota: an evolutionary medicine perspective – Molly Fox – Annals of the New York Academy of Sciences

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis – Jessica L. Mark Welch – Annual Review of Microbiology

Human microbiome

Colonic mucosal and exfoliome transcriptomic profiling and fecal microbiome response to a flaxseed lignan extract intervention in humans – Johanna W. Lampe – American journal of Clinical Nutrition

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals – Riccardo Vasapolli – Gastroenterology

Identification of Salivary Microbiota and its Association with Host Inflammatory Mediators in Periodontitis – Anna Lundmark – Frontiers in Cellular and Infection Microbiology

Effect of the Degree of Polymerization of Fructans on Ex Vivo Fermented Human Gut Microbiome – Erola Astó – Nutrients

Inflammatory skin is associated with changes in the skin microbiota composition on the back of severe acne patients – Marie-Ange Dagnelie – Experimental Dermatology

Gut microbiota development of preterm infants hospitalised in intensive care units – H. Tauchi – Beneficial Microbes

Animal experiments

Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota – Devin B. Holman – Microbiome

Sequential changes in the host gut microbiota during infection with the intestinal parasitic nematode Strongyloides venezuelensis – Tanzila Afrin – Frontiers in Cellular and Infection Microbiology

Plant, root, soil microbiome

A global survey of arsenic-related genes in soil microbiomes – Taylor K. Dunivin – BMC Biology

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics – Nengfei Wang – Microbes and Environments

Water microbiome and extremophiles

Comparison of the microbiomes of two drinking water distribution systems—with and without residual chloramine disinfection – Michael B. Waak – Microbiome

Probiotics

Probiotics may not prevent the deterioration of necrotizing enterocolitis from stage I to II/III – Zheng-Li Wang – BMC Pediatrics

Bifidobacterium bifidum and the infant gut microbiota: an intriguing case of microbe‐host co‐evolution – Sabrina Duranti – Environmental Microbiology

Techniques

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes – G.A.Arango-Argoty – Microbiome

Metabolic route computation in organism communities – Markus Krummenacker – Microbiome

The role of multilevel selection in host microbiome evolution – Simon van Vliet – BioRxiv

Microbes and the market

Human Microbiome Therapeutics Market Analysis 2019: With Top 20 Countries data, Product Types, Segmentation, Market Share Analysis, Influential Trends And Challenges, Forecast To 2023 – Saginaw Daily

Global Human Microbiome Based Drugs and Diagnostics Market Potential Growth 2019 | Second Genome Inc., Enterome Bioscience, Yakult – Business Tech Hub

Human Microbiome Market 2024 Significant Development | Future Trends of Key Players by Size and Share – The Warren Daily

In-Depth Research Report of Global Microbiome Sequencing Services Market (2019 Version), with Types, Application, and Manufactures – the Pueblo Daily

Microbiome Sequencing Services Market Key Players, Industry Overview, Demand & Supply Chain Analysis, Forecast To 2024 – Burbank Observer

Human Microbiome Market Growth, Trend and Forecast 2018-2026 – Business Herald

 

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June 10, 2019

This Monday, read about the precision of microbiome wording, cryopreservation of the human gut microbiota, water infrastructure microbiomes, and more. Happy reading!

General microbiome

Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers – Kim M. Handley – mSystems

Digitalizing the Microbiome for Human Health – Kirti Nath and Christoph A. Thaiss – mSystems

New Approaches to Microbiome-Based Therapies – Andrea C. Wong and Maayan Levy – mSystems

Benefits and Costs of Animal Virulence for Microbes – Arturo Casadevall and Liise-anne Pirofski – mSystems

*Language, numeracy and logic in microbiome science – Fergus Shanahan and Colin Hill – Nature Reviews Gastroenterology & Hepatology

Gut microbiome

*Cryopreservation of the human gut microbiota: current state and perspectives – Daria V.Smirnovaa – International Journal of Medical Microbiology

Metaproteomics of the human gut microbiota: challenges and contributions to other OMICS – Ngom Issa Isaac – Clinical Mass Spectrometry

Mapping human microbiome drug metabolism by gut bacteria and their genes – Michael Zimmermann – Nature

MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing – William S Taylor – bioRxiv

Assessment of Causal Direction Between Gut Microbiota-Dependent Metabolites and Cardiometabolic Health: Abi-Directional Mendelian Randomisation Analysis – Jinzhu Jia – Diabetes

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer – Shinichi Yachida – Nature Medicine

Dysbiosis of gut microbiota in a selected population of Parkinson’s patients – Daniele Pietrucci – Parkinsonism & Related Disorders

Animal experiment

Heterochronic faecal transplantation boosts gut germinal centres in aged mice – Marisa Stebegg – Nature communications

High fat diet alters gut microbiota but not spatial working memory in early middle-aged Sprague Dawley rats – Nikita Girish Deshpande – PlosOne

Animal microbiome

Fibre digestion by rumen microbiota – a review of recent metagenomic and metatranscriptomic studies – Stephanie A Terry – Canadian Journal of Animal Science

Correlation between Disease Severity and the Intestinal Microbiome in Mycobacterium tuberculosis-Infected Rhesus Macaques – Sivaranjani Namasivayam – mBio

Water microbiome

*Integrating biotechnology and microbial ecology in urban water infrastructure through a microbiome continuum viewpoint – Lutgarde Raskin and Per Halkjær Nielsen – Current Opinion in Biotechnology

Techniques

MOBN: an interactive database of multi-omics biological networks – Cheng Zhang – bioRxiv

June 4, 2019

General microbiome
Rigorous Statistical Methods for Rigorous Microbiome Science – Amy D. Willis – mSystems

Understanding microbial community dynamics to improve optimal microbiome selection – Robyn J. Wright – Microbiome

Toward a Better Understanding of Species Interactions through Network Biology – Ryan S. McClure – mSystems

Human respiratory microbiome
Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus – Hyun Jik Kim – Microbiome

Human gut microbiome
A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans – Alfonso Benítez-Páez – mSystems

Gut microbiome identifies risk for colorectal polyps – Ezzat Dadkhah – BMJ Open Gastroenterology

Yogurt improves insulin resistance and liver fat in obese women with nonalcoholic fatty liver disease and metabolic syndrome: a randomized controlled trial – Yang Chen – American Journal of Clinical Nutrition

Preprint: Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids – Robert A Quinn – bioRxiv

Animal models
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model – Limei Lin – Microbiome

Missing Links: the Role of Primates in Understanding the Human Microbiome – Katherine R. Amato – mSystems

Plant, root, and soil microbiome
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays – Frank Reith – Annals of Botany

Water and extremophile microbiome
Effects of sulfamethoxazole and sulfamethoxazole-degrading bacteria on water quality and microbial communities in milkfish ponds – Bea-Ven Chang – Environmental Pollution

Preprint: Temporal dynamics of Bacteria, Archaea and protists in equatorial coastal waters – Caroline Chénard – bioRxiv

Built environment
Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area – Miles Richardson – Microbiome

Phages and viruses
Preprint: The human gut virome is highly diverse, stable and individual-specific – Andrey Shkoporov – bioRxiv

Bioinformatics
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language – Luis Pedro Coelho – Microbiome

Science, publishing, and career
Preprint: The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Rochelle E. Tractenberg – bioRxiv

Alyson’s non-microbiology picks
Why Your Metro Commute Is So Insanely Windy – Julie Bogen – The Atlantic

The 2019 Wellcome photography prize: close focus on the human condition – Sean O’Hagan – The Guardian

May 29, 2019

Changes to the pig gut microbiome based on age, gut bacteria community composition in aquatic invertebrates, fungal diversity on limestone cathedral walls, chalk-talk vs PowerPoint in large microbiology lectures.

Human oral microbiome

Applications of the oral microbiome in personalized dentistry – Georgios N Belibasakis – Archives of Oral Biology

Human vaginal microbiome

Detection of Methanobrevibacter smithii in vaginal samples collected from women diagnosed with bacterial vaginosis – Ghiles Grine – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Gut Microbial Dataset of a foraging tribe from rural West Bengal – insights into unadulterated and transitional microbial abundance – Sayak Ganguli – Data in Brief

Gut microbiome of pre-adolescent children of two ethnicities residing in three distant cities – Wei Wei Thwe Khine – Scientific Reports

The eradication of Helicobacter pylori restores rather than disturbs the gastrointestinal microbiota in asymptomatic young adults – Cong He – Helicobacter

Pre-print: Cytometric fingerprints of gut microbiota predict Crohn’s disease state – Peter Rubbens – bioRxiv

Animal experiments

Rapamycin modulates tissue aging and lifespan independently of the gut microbiota in Drosophila – Joseph M Schinaman – Scientific Reports

Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition – Shanlin Ke – BMC Veterinary Research

Pre-print: Effects of Five Products on Gut Microbiota and Short-Chain Fatty Acids of Obese Rats – Simin Tan – bioRxiv

Animal microbiome

Effect of different forage-to-concentrate ratios on ruminal bacterial structure and real-time methane production in sheep – Runhang Li – PLOS ONE

Pre-print: Microbiomes from feces vs. gut in aquatic vertebrates: distinct community compositions between substrates and preservation methods – Sten Anslan – bioRxiv

Plant, root, and soil microbiome

Glycoside Hydrolase Genes Are Required for Virulence of Agrobacterium tumefaciens on Bryophyllum daigremontiana and Tomato – Stephanie L Mathews – Applied and Environmental Microbiology

Effect of water-driven changes in rice rhizosphere on Cd lability in three soils with different pH – Jinjin Wang – Journal of Environmental Sciences

Impact of AMF Claroideoglomus etunicatum on the structure of fungal communities in the tomato rhizosphere – Agnieszka Jamiołkowska – Acta Mycologica

Effect of land use and carbonates on organic matter stabilization and microbial communities in Mediterranean soils – Mireia Martí-Roura – Geoderma

Pre-print: Close-Range Interactions Favor Growth in Random-Paired Extracted Soil Bacteria – Manupriyam Dubey – bioRxiv

Water and extremophile microbiome

New microbial lineages capable of carbon fixation and nutrient cycling in deep-sea sediments of the northern South China Sea – Jiao-Mei Huang – Applied and Environmental Microbiology

Pre-print: Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep – Guojie Cui – PeerJ

Taxonomic structure and potential nitrogen metabolism of microbial assemblage in a large hypereutrophic steppe lake – Xiaodong Qu – Environmental Science and Pollution Research

Built environment

Fungal diversity and distribution across distinct biodeterioration phenomena in limestone walls of the old cathedral of Coimbra, UNESCO World Heritage Site – João Trovão – International Biodeterioration & Biodegradation

Probiotics/prebiotics

Dietary probiotics have different effects on the composition of fecal microbiota in farmed raccoon dog (Nyctereutes procyonoides) and silver fox (Vulpes vulpes fulva) – Yongjia Peng – BMC Microbiology

Microbes in the news

Microbiome therapies could be the next frontier in medicine. But how exactly do you make them? – Kate Sheridan – STAT

Possible link between infant gut microbiome and development of allergies – Bob Yirka – Medical Xpress

Science, career, and publishing

Pre-print: Rock the Chalk: A five-year comparative analysis of a large microbiology lecture course reveals improved outcomes of chalk-talk compared to PowerPoint – Christopher M Waters – bioRxiv

May 28, 2019

Today’s digest is about metaproteomics in microbial communities, infant and child microbiome and association with diseases, coral ecosphere, microbial biospherics and updates on new techniques to analyze microbiome sequencing data.

General microbiome

Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities – Manuel Kleiner – mSystems

Associational effects in the microbial neighborhood – Anja Worrich – ISME Journal

Uncovering complex molecular networks in host–pathogen interactions using systems biology – Joshua M. Peters – Emerging Topics in Life Sciences

Human microbiome

The skin microbiome of vertebrates – Ashley A. Ross – Microbiome

Patterns in the longitudinal oropharyngeal microbiome evolution related to ventilator-associated pneumonia – Rami Sommerstein – Antimicrobial Resistance & Infection Control

Microbial composition of the human nasopharynx varies according to influenza virus type and vaccination status – Tao Ding -BioRxiv

Cytometric fingerprints of gut microbiota predict Crohn’s disease state – Peter Rubbens – BioRxiv

Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease – Nathaniel D. Chu – BioRxiv

Pregnancy and infant microbiome

Paediatrician’s perspective of infant gut microbiome research: current status and challenges – Paul MacDaragh Ryan – Archives of Disease in Childhood

The Salivary Microbiome Is Altered in Children With Eosinophilic Esophagitis and Correlates With Disease Activity – Hiremath Girish – Clinical and Translational Gastroenterology

Influence of own mother’s milk and different proportions of formula on intestinal microbiota of very preterm newborns – Adriana Zanella – PlosOne

Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates – Esperanza Escribano – PlosOne

Reviewing the evidence on breast milk composition and immunological outcomes – Alba Boix-Amorós – Nutrition Reviews

Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis – Rafal Tokarz – Inflammatory Bowel Diseases

Animal experiments

Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio – Pei P. Fu – Parasites and Vectors

Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and their Functional Annotations – Himanshu Kumar – Genes

Toll‐like receptor 2 and toll‐like receptor 4 responses regulate neutrophil infiltration into the junctional epithelium and significantly contribute to the composition of the oral microbiota – Ana M. Chang – Journal of Periodontology

Plant, root, soil microbiome

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms – Spencer Diamond – Nature Microbiology

Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin – Allison M. Veach – Microbiome

Microbial community drivers of PK/NRP gene diversity in selected global soils – Chiara Borsetto – Microbiome

Decreased temporary turnover of bacterial communities along soil depth gradient during a 35-year grazing exclusion period in a semiarid grassland – Chao Zhang – Geoderma

Soil bacterial community dynamics following surfactant addition and bioaugmentation in pyrene-contaminated soils – D.C.Wolf – Chemosphere

Structural and Functional Responses of Soil Microbial Communities to Biodegradable Plastic Film Mulching in Two Agroecosystems – Sreejata Bandopadhyay – BioRxiv

Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons – Tess E. Brewer – BioRxiv

Water microbiome and extremophiles

The coral ecosphere: A unique coral reef habitat that fosters coral–microbial interactions – Laura Weber – Limnology and Oceanography

Tide driven microbial dynamics through virus-host interactions in the estuarine ecosystem – Xiaowei Chen – Water Research

Microbial biofilm formation and community structure on low-density polyethylene microparticles in lake water microcosms – Mengting Gong – Environmental Pollution

Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone – Evan Lau – PlosOne

Consistent metagenome-derived metrics verify and define bacterial species boundaries – Matthew R. Olm – BioRxiv

Techniques

Competitive interaction with keystone taxa induced negative priming under biochar amendments – Lijun Chen – Microbiome

Strengthening Insights in Microbial Ecological Networks from Theory to Applications – Xiaofei Lv – mSystems

Microbial biospherics: The experimental study of ecosystem function and evolution Matthias C. Rillig – PNAS

NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities – Bowen Li – BioRxiv

Detecting interaction networks in the human microbiome with conditional Granger causality – Kumar Mainali – Plos Computational Biology

M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data – Oren Avram – Nucleic Acids Research

End-to-end assessment of fecal bacteriome analysis: from sample processing to DNA sequencing and bioinformatics results – Ana Paula Christoff – BioRxiv

Microbiome in news

Antibiotics may help curb Alzheimer’s symptoms – Medical News Today

SANISCALP®, to preserve the Microbiome for a soothed and healthy scalp! – Cosmetics desgin.com – Mamamia

Mother Dirt Expands Biome-Friendly Skincare Range With New Body Care Line – Mid Daily News

Microbes and the market

Global Microbiome Drugs Market Forecast 2019-2025: MaaT Pharma, Pfizer, Second Genome, Seres Therapeutics – Technology Market

Microbiome Therapeutics Market 2019 – By Future Growth, Trends Plans, Top Key Players, Business Opportunities, Region, Pricing Analysis, Opportunities and Forecast to 2024 – Norwalk Daily

Global Human Microbiome Modulators Market Report 2019: Trends and Opportunities for the Business Prediction over 2024 – Current News Magazine

Microbiome Sequencing Services Market 2019 Report Shows the Competitive Situation Among the Top Manufacturers, With Sales, Revenue and Share – Augusta Observer

 

May 23, 2019

Composition of the human mucosa-associated microbiota, changes in gut microbial diversity with social rank in cichlid fish, microbes supporting sustainable rice production, the effects of tweeting on article engagement in medical education.

General microbiome

Global change microbiology — big questions about small life for our future – Antje Boetius – Nature Reviews Microbiology

Human oral microbiome

Review: The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease – Alex M Valm – Journal of Molecular Biology

Human gut microbiome

Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps – Florent Ailloud – Nature Communications

Pre-print: Complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids – Thomas V Syndenham – bioRxiv

Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals – FER Vuik – United European Gastroenterology Journal

Animal experiments

Loss of function dysbiosis associated with antibiotics and high fat, high sugar diet – Aaron W Miller – The ISME Journal

Saccharomyces boulardii CNCM I-745 changes lipidemic profile and gut microbiota in a hamster hypercholesterolemic model – F Briand – Beneficial Microbes

Animal microbiome

Gut microbial diversity increases with social rank in the African cichlid fish, Astatotilapia burtoni – Avehi Singh – Animal Behaviour

Amphibian Host and Skin Microbiota Response to a Common Agricultural Antimicrobial and Internal Parasite – Obed Hernández-Gómez – Microbial Ecology

Pre-print: Space, time, and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate – Sarah E Haworth – bioRxiv

Plant, root, and soil microbiome

Interaction between root hairs and soil phosphorus on rhizosphere priming of soil organic matter – Gabriel Boilard – Soil Biology and Biochemistry

Green manures of Indian mustard and wild rocket enhance cucumber resistance to Fusarium wilt through modulating rhizosphere bacterial community composition – Xue Jin – Plant and Soil

Ozone dose-response relationships for soil microbial dynamics of winter wheat in North China – Enzhu Hu – Atmospheric Environment

Water and extremophile microbiome

Filamentous calcareous alga provides substrate for coral-competitive macroalgae in the degraded lagoon of Dongsha Atoll, Taiwan – Carolin Nieder – PLOS ONE

Food microbiology

Roles of microbes in supporting sustainable rice production using the system of rice intensification – Febri Doni – Applied Microbiology and Biotechnology

Microbes in the news

Airway microbiome appears altered in severe asthma linked to neutrophils – EurekAlert

Coffee Consumption Alters Microbiome and Improves Gut Motility – Genetic Engineering & Biotechnology News

Researchers receive $1.94 million to study connection between autism, microbiome – EurekAlert

Novel Autonomous Biosampler Will Foster In Situ Aquatic Microbiome Monitoring – Eunice Sousa – Science Trends

Meta-study suggests anxiety can be reduced by altering gut bacteria, but not with probiotics – Rich Haridy – New Atlas

Science, career, and publishing

Pre-print: To Tweet or Not to Tweet, That is the Question: A Randomized Trial of Twitter Effects on Article Engagement in Medical Education – Lauren A Maggio – bioRxiv

May 22, 2019

Today’s Digest is full of new perspectives on appropriate models and techniques, including the future of gnotobiotics and using unbiased metagenomics to find RNA viruses. There are also several plant, root, and soil papers, particularly examining the interplay between bacterial and fungal communities. Finally, enjoy a preprint about the cartography of antibiotic resistance genes in a hospital, a study examining the microbiota in larval mosquito vectors of malaria, and a paper about the microeukaryotes associated with coral reefs.

General Microbiome
Review: Antibiotics versus biofilm: an emerging battleground in microbial communities – Divakar Sharma – Antimicrobial Resistance & Infection Control

Review: Gnotobiotics: Past, present and future – Marijana Basic – Laboratory Animals

Review: The use of non-rodent model species in microbiota studies – Aaron C. Ericsson – Laboratory Animals

Pregnancy and Early Life
Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates – Esperanza Escribano – PLoS One

Human Vaginal Microbiome
Vaginal microbiota and mucosal pharmacokinetics of tenofovir in healthy women using tenofovir and tenofovir/levonorgestrel vaginal rings – Andrea Ries Thurman – PLoS One

Human Oral Microbiome
Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function – Claire Duvallet – PLoS One

Animal Microbiome
Color morphology of Diaphorina citri influences interactions with its bacterial endosymbionts and ‘Candidatus Liberibacter asiaticus’ – Saeed Hosseinzadeh – PLoS One

Conspecific coprophagy stimulates normal development in a germ-free model invertebrate – Benjamin C. Jahnes – PeerJ

Malaria vector species in Amazonian Peru co-occur in larval habitats but have distinct larval microbial communities – Catharine Prussing – PLoS Neglected Tropical Diseases

Animal Experiments
Gut and immune effects of bioactive milk factors in preterm pigs exposed to prenatal inflammation – Shuqiang Ren – American Journal of Physiology-Gastrointestinal and Liver Physiology

Effects of oregano essential oil on the ruminal pH and microbial population of sheep – Rui Zhou – PLoS One

Plant, Root, and Soil Microbiome
Characterizing the intra-vineyard variation of soil bacterial and fungal communities – Hebin Liang – Frontiers in Microbiology

The role of fungi in heterogeneous sediment microbial networks – Jenny Marie Booth – Scientific Reports

Altering N2O emissions by manipulating wheat root bacterial community – Alla Usyskin-Tonne – Scientific Reports

Sphingomonas sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis Thaliana Under Drought Stress – Yang Luo – Frontiers in Microbiology

Enrichment of soil rare bacteria in root by an invasive plant Ageratina adenophora – Lin Chen – Science of the Total Environment

Effect of rhizospheric and endophytic bacteria with multiple plant growth promoting traits on wheat growth – Somayeh Emami – Environmental Science and Pollution Research

Water and Extremophile Microbiome
A comparison of microeukaryote communities inhabiting sponges and seawater in a Taiwanese coral reef system – Daniel Francis Richard Cleary – Annals of Microbiology

An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa – K. Jordaan – PLoS One

Built Environment
Preprint: Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment – Kern Rei Chng – bioRxiv

Fungal community composition analysis of 24 different urban parks in Shanghai, China – Jing Zhang – Urban Ecosystems

Techniques
Expanding the RNA Virosphere by Unbiased Metagenomics – Yong-Zhen Zhang – Annual Review of Virology

Preprint: Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO – Alexander H. Wilcox – bioRxiv

Development of an autonomous biosampler to capture in situ aquatic microbiomes – Hugo Ribeiro – PLoS One