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 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

June 2, 2019

Highlights: Harnessing principles of ecology and engineering in building microbiome, community ecology perspective of human microbiome, rhizospheric microbes, soil viruses and many more.

General microbiome

Regulating microbiome manipulation – Kjersti Aagaard – Nature Medicine

Towards a Better Understanding of Microbial Community Dynamics through High-Throughput Cultivation and Data Integration – Karoline Faust – mSystems

Reconciling Ecological and Engineering Design Principles for Building Microbiomes – Hans C. Bernstein – mSystems

Community ecology as a framework for human microbiome research – Jack A Gilbert – Nature Medicine

Multi-site human microbiome

Age-dependent dissimilarity of the nasopharyngeal and middle ear microbiota in children with acute otitis media – Silvio D. Brugger – Frontiers in Genetics

Human gut microbiome

Micronutrient requirements and sharing capabilities of the human gut microbiome – Dmitry A Rodionov – Frontiers in Microbiology

Animal experiments 

Mouse microbiomes: overlooked culprits of experimental variability – Maria-Luisa Alegre – Genome Biology

Animal microbiome 

Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis – S. Dalvin – Marine Genomics

Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health – Keylie M. Gibson – Scientific Reports

Not all animals need a microbiome – Tobin J Hammer – FEMS Microbiology Letters

The Microbiome of the Maculinea-Myrmica Host-Parasite Interaction – Marco Di Salvo – Scientific Reports

Plant, root, and soil microbiome

Soil photosynthetic microbial communities mediate aggregate stability: influence of cropping systems and herbicide use in an agricultural soil – Olivier Crouzet – Frontiers in Microbiology

Fluazinam positively affected the microbial communities in clubroot cabbage rhizosphere – Chunming Liu – Scientia Horticulturae

Soil microbiome mediates positive plant diversity‐productivity relationships in late successional grassland species – Guangzhou Wang – Ecology Letters

A water stress-adapted inoculum affects rhizosphere fungi, but not bacteria nor wheat – Charlotte Giard-Laliberté – Microbiology Ecology

Variations in phyllosphere microbial community along with the development of angular leaf-spot of cucumber – Luyun Luo – AMB Express

Built environment 

Effects of biochar on the phenol treatment performance and microbial communities shift in sequencing batch reactors – Shengnan Shi – Water Research

Effects of ozone treatment on performance and microbial community composition in biofiltration systems treating ethyl acetate vapours – Itzel Covarrubias-García – Chemosphere

Phages and viruses

Characterization of the virome of Paracoccus spp. (Alphaproteobacteria) by combined in silico and in vivo approaches – Przemyslaw Decewicz – Scientific Reports

Soil Viruses: A New Hope – Joanne B. Emerson – mSystems

 

May 31, 2019

Happy Friday!! Today’s digest contains reviews on the role of microbiota in immune memory formation and bioinformatic tools for soil microbiome analysis

General microbiome

*Review: The microbiome and immune memory formation – Kathy D. McCoy – Immunology and Cell biology

Preprint – Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing – Emily Crawford – bioRxiv

Animal experiments

Response of Fish Gut Microbiota to Toxin-Containing Cyanobacterial Extracts: A Microcosm Study on the Medaka (Oryzias latipes) – Sébastien Duperron – Environmental Science & Technology Letters

Plant, root, and soil microbiome

*Book chapter : Bioinformatics Tools for Soil Microbiome Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Belowground Microbial Communities: Key Players for Soil and Environmental Sustainability – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Single-Cell Genomics and Metagenomics for Microbial Diversity Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

In vitro digestion and fermentation of three polysaccharide fractions from Laminaria japonica and their impact on lipid metabolism-associated human gut microbiota – Jie Gao – Journal of Agricultural and Food Chemistry

Preprint – Biogeographical patterns in soil bacterial communities across the Arctic region – Lucie A Malard – bioRxiv

Water and extremophile microbiome

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient – Marie Simonin – Environmental Microbiology

Phages and viruses

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages – Jakub Barylski – Systematic Biology

Techniques

Protocol: Analysis of Microbial Siderophores by Mass Spectrometry – Tomas Pluhacek – Part of the Methods in Molecular Biology

Review: A guide to visualizing the spatial epigenome with super‐resolution microscopy – Jianquan Xu – The FEBS Journal

May 30, 2019

How the cheese rind microbiome diversity affects function, development of “metabolic overlap” as a metric to assess different microbial communities using genomic information, a variety of research articles, commentaries, press releases, and news stories covering the NIH Human Microbiome Project at the completion of its second phase.

General microbiome

Homepage for “Human Microbiome Project, part 2” special section in Nature including:

Human vaginal microbiome

The vaginal microbiome and preterm birth – Jennifer M Fettweis – Nature Medicine

Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy – Myrna G Serrano – Nature Medicine

Human gut microbiome

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases – Jason Lloyd-Price – Nature

Pre-print: Antioxidants maintain Butyrate production by Human Gut Clostridia in the presence of Oxygen – Matthieu Million – bioRxiv

A microbiota-generated bile salt induces biofilm formation in Clostridium difficile – Thomas Dubois – NPJ Biofilms and Microbiomes

Plant, root, and soil microbiome

Pre-print: Bacterial and fungal communities are differentially modified by melatonin in agricultural soils under abiotic stress – Andrew P Madigan – bioRxiv

Food microbiology

Pre-print: Strain-level diversity impacts cheese rind microbiome assembly and function – Brittany A Niccum – bioRxiv

Bioinformatics

Pre-print: Metabolic overlap in environmentally diverse microbial communities – Eric R Hester – bioRxiv

Microbes in the news

The Human Microbiome Project expands the toolbox for studying host and microbiome interactions – National Institutes of Health

A wave of NIH-backed microbiome research examines the gut’s link to diabetes, inflammatory bowel disease, and more – Kate Sheridan – STAT

Human Microbiome Project reveals how microbiome is disrupted during inflammatory bowel disease – Christopher Sweeney – Broad Institute

Scientists Find Bacteria Thriving In Earth Environment That’s Just Like Young Mars – Aristos Georgiou – Newsweek

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