February 4, 2018

The publication of a Springer manual entitled Mechanisms underlying host-microbiome interactions in pathopysiology of human diseases contains multiple interesting articles today, including reviews on the gut microbiome and preterm infant gut development, colerectal cancer, and metabolic disease, as well as a useful review of statistical models for mouse and human microbiome data. In addition, a revisitation of gut enterotypes via metabolomics, decreased Akkermansia muciniphila in psoriasis, the bacterial communities of fiddler crabs, the impact of different wavelengths of light on hot spring bacteria, and two articles on the uses of metabarcoding in both 16S and eukaryotic microbiota analysis.

Events and jobs

Microbiology Manager – Covance – Indianapolis, Indiana

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Pregnancy and early life

*Review: Impact of Microbes on the Intestinal Development of the Preterm Infant – Elizabeth Humphrey – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Multi-site human microbiome

Review: Good and Bad Farming: The Right Microbiome Protects from Allergy – Markus Johannes Ege – Allergy Prevention and Exacerbation

Human gut microbiome

*Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes – Manoj Kumar Verma – Scientific Reports

Gastric bacterial Flora in patients Harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy – Verima Pereira – BMC Gasteroentrology

*The Akkermansia muciniphila is a gut microbiota signature in psoriasis – LiRong Tan – Experimental Dermatology

Review: The regulation of host cellular and gut microbial metabolism in the development and prevention of colorectal cancer – Cheng-Bei Zhou – Critical Reviews in Microbiology

Editorial: Unveiling the gut virome in human health and diseases – Tao Zuo – International Journal of Clinical Virology

*Review: The Influence of the Microbiota on the Etiology of Colorectal Cancer – Melissa C. Kordahi – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

*Review: Altered Microbiota and Their Metabolism in Host Metabolic Diseases – Beng San Yeoh – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Review: The Gut Microbiome and Its Marriage to the Immune System: Can We Change It All? – Eva Untersmayr – Allergy Prevention and Exacerbation

*Review: Fecal Microbiota Transplants: Current Knowledge and Future Directions – Roxana Chis – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

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Animal experiments

Tissue Level Diet and Sex-by-Diet Interactions Reveal Unique Metabolite and Clustering Profiles Using Untargeted Liquid Chromatography-Mass Spectrometry on Adipose, Skeletal Muscle, and Liver Tissue in C57BL6/J Mice – Ann Wells – Journal of Proteome Research

The Changes of Colonic Bacterial Composition and Bacterial Metabolism Induced by an Early Food Introduction in a Neonatal Porcine Model – Chao Shi – Current Microbiology

Animal microbiome

*Multiple colonist pools shape fiddler crab-associated bacterial communities – Catalina Cuellar-Gempeler – The ISME Journal

Transcriptional changes detected in fecal RNA of neonatal dairy calves undergoing a mild diarrhea are associated with inflammatory biomarkers – Fernanda Rosa – PLOSone

Tiny but mighty: The role of the rumen microbes in livestock production
K M Cammack – Journal of Animal Science

Effects of Spray-Dried Porcine Plasma on Fecal Microbiota in Nursery Pigs – Huyen Tran – Journal of Animal Science

Organic acid production from potato starch waste fermentation by rumen microbial communities from Dutch and Thai dairy cows – Susakul Palakawong Na Ayudthaya – Biotechnology for Biofuels

Plant, root, and soil microbiome

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C. A. Mallon – The ISME Journal

Stress-Tolerant Beneficial Microbes for Sustainable Agricultural Production – Reeta Goel – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 7. Springer

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire – Taylor K. Dunivin – PLOSone

Review: The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance – Msizi Mhlongo – Frontiers in Plant Science

Characterization of bacteria isolated from the Saffron (Crocus Sativus L.) rhizosphere – Majid Jami Al-Ahmadi – Journal of Horticultural Research

Review: Rhizoremediation – Plant Microbe Interactions in the Removal of Pollutants – Mehak Oberai – International Journal of Current Microbiology and Applied Sciences (IJCMAS)

Role of microbes in organic carbon decomposition and maintenance of soil ecosystem – Hina Khatoon – International Journal of Chemical Studies

Water and extremophile microbiome

Vibrio cholerae embraces two major evolutionary traits as revealed by targeted gene sequencing – Kazuhisa Okada – Scientific Reports

*Effect of light wavelength on hot spring microbial mat biodiversity – Akifumi Nishida – PLOSone

Microbial Ecology

Estimating taxon-specific population dynamics in diverse microbial communities – Benjamin J. Koch – Ecosphere

Metabolomic analysis of low and high biofilm-forming Helicobacter pylori strains – Eric Hong Jian Wong – Scientific Reports

Resistome

High dietary zinc feeding promotes persistence of multi-resistant E. coli in the swine gut – Lisa Ciesinski – PLOSone

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Probiotics / prebiotics

An Integrative Review on the Effect of Prebiotics, Probiotics, and Synbiotics on Infection After Colorectal Cancer Surgery – Sarah Williams Anderson – Aorn Journal

Phages and Viruses

Metagenomic Analysis of the Jinding Duck Fecal Virome – Lili Zhao – Current Microbiology

Bioinformatics

*Statistical Models and Analysis of Microbiome Data from Mice and Humans – Yinglin Xia – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases – Qingyu Chen – Journal of Data and Information Quality

Techniques

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving – Clinical Metabolomics

*16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer) – Clare Bird – PLOSone

*Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients – Ibrahim Hamad – PLOSone

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Microbes in the news

The Germ and the Gene: Gut Bacteria Research Takes a Step Forward – Ruairi MacKenzie – Technology Networks

These bacteria produce gold by digesting toxic metals – EurekaAlert

January 28, 2018

Posted on January 28, 2018 by Kiran

A preprint on the gut microbiome of few tribal groups in the Himalayan region; association between vaginal microbiota and HIV; an integrative approach that encompasses metatranscriptomics & fatty acid profiling to study the rumen microbiome during feeding; environmental adaptation shapes the gut microbiota of Rhesus macaques; microbiome of cactus rhizosphere; news about uBiome; antibiotics; and many more articles for today’s digest!

Building Bioeconomy in Agriculture: Harnessing Soil Microbes for Sustaining Ecosystem Services – R Rengalakshmi – Towards a Sustainable Bioeconomy: Principles, Challenges and Perspectives

Competitive traits are more important than stress-tolerance traits in a cadmium-contaminated rhizosphere: a role for trait theory in microbial ecology – JL Wood – Frontiers in Microbiology

Draft Genome Sequence of Pantoea ananatis Strain 1.38, a Bacterium Isolated from the Rhizosphere of Oryza sativa var. Puntal That Shows Biotechnological Potential as an Inoculant – E Megías – Genome Announcements

Copper Bioleaching in China: Review and Prospect – S Yin – Minerals

Water microbiome and extremophiles

Core promoter information content correlates with optimal growth temperature – AA Aptekmann – Scientific Reports

Food microbiology

Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening – M Olvera-García – Applied Microbiology and Biotechnology

Phages and viruses

Review: Phage or foe: an insight into the impact of viral predation on microbial communities – L Fernández – The ISME Journal

Techniques

Artificial Gene Amplification in Escherichia coli Reveals Numerous Determinants for Resistance to Metal Toxicity – KJ Hoegler – Journal of Molecular Evolution

Microbes in the news

uBiome, the Leader in Microbial Genomics, Launches SmartGut and SmartJane Microbiome Test Kits in Canada – Daily Telescope

Niki Bezzant: A gutsful of good health – NZ Herald

How Phenylbutazone, Firocoxib Affect Horses’ Gut Microbiota – the Horse

Botulinum-type toxins jump to a new kind of bacteria – Science Daily

‘Forgotten’ antibiotic offers hope against worst superbugs – Digital Journal

Detect The Level Of Bacteria In Food With This Smartphone-Based System – Wonderful Engineering

When bad bugs jump from farm to bedside – Hutch News

January 27, 2018

Posted on January 27, 2018 by Kiran

A Saturday digest with lots of fun and weird news of microbiome!

Events and jobs

Adjunct Faculty- Biology, Microbiology, Anatomy & Physiology – St. Louis Community College in Missouri – USA

General microbiome

A Case of Recurrent Pasteurella Bacteremia in an Immunocompetent Patient with No Animal Bite. – F Zarlasht – The American Journal of Case Reports

Pregnancy and early life

Lipopolysaccharide-induced maternal inflammation induces direct placental injury without alteration in placental blood flow and induces a secondary fetal intestinal injury that persists into adulthood. – EM Fricke – American Journal of Reproductive Immunology

Association between duration of intravenous antibiotic administration and early-life microbiota development in late-preterm infants – RD Zwittink – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach – FM Borges – Current Microbiology

Review: Dietary practices and FODMAPs in South Asia: Applicability of the low FODMAP diet to patients with irritable bowel syndrome – SP Hewawasam – Journal of Gastroenterology and Hepatology

Animal experiments

Preprint: Mono-Association with Lactobacillus plantarum Disrupts Intestinal Homeostasis in adult Drosophila. – D Fast – bioRxiv

Beneficial effects of Rifaximin in post-infectious irritable bowel syndrome mouse model beyond gut microbiota – Y Jin – Journal of Gastroenterology and Hepatology

Plant, root and soil microbiome

Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves. – EJ Canter – Ecology

Purple corn-associated rhizobacteria with potential for plant growth promotion – A Castellano-Hinojosa – Journal of Applied Microbiology

Fungal diversity in oil palm leaves showing symptoms of Fatal Yellowing disease – OY de Assis Costa – PLoS One

Biosynthetic and antimicrobial potential of actinobacteria isolated from bulrush rhizospheres habitat in Zhalong Wetland, China – Y Li – Archives of Microbiology

Effect of Silene vulgaris and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil – M Pacwa-Płociniczak – Water, Air and Soil Pollution

Water microbiome and extremophile

Ecological and biogeographical drivers of freshwater green algae biodiversity: from local communities to large-scale species pools of desmids – H Bestová – Oecologia

Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide – A Nishihara – J-Stage

Food microbiology

Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing – HNJ Shangpliang – Scientific Reports

Phages and viruses

Preprint: Diversity and evolution of the emerging Pandoraviridae family – M Legendre – bioRxiv

Microbes in the news

Explore the human microbiome in new Delaware natural history museum exhibit – Delaware Public Media

Thoroughness of panel called into question – Delta Optimist

When DNA Went Mobile Some Archaea Jumped Out of the Hot Tub – GEN News

Scientists find 10 new defense systems used by bacteria – Science News

ASTRONAUTS LIVING IN SPACE CAN EAT BACTERIA THAT FEED ON HUMAN WASTE – Newsweek

A Never-Before-Seen Virus Was Just Found in the Sea, and It Kills Bacteria – Inverse Science

Bacteria block transmission of Zika and Dengue viruses – Medical Xpress

First annual thesis competition held at JMU – The Breeze

Microbiome research refines HIV risk for women – EurekAlert

Shimmery bacteria plus a canvas equals art, briefly – Chicago Tribune

BACTERIA THAT HITCH RIDES ON TOOTHBRUSHES, DIAPERS AND OTHER PLASTIC POLLUTION ARE KILLING CORAL REEFS – Newsweek

January 26, 2018

Posted on January 26, 2018 by xinhuang7

Here’s your daily Digest after a burst of articles. High-intensity swimming can impact immunity and microbial diversity in mice. Intestinal microbiota can alter host epigenetic in mice. A sad story of an eight year old boy killed by flesh eating bacteria…

Jobs and events

The Human Microbiome – Heidelberg, Germany

2018 MICROBIOME CONFERENCES – Taconic

General microbiology

Peptidoglycan compositional analysis of Enterococcus faecalis biofilm by stable isotope labeling by amino acids in bacterial culture – James D. Chang et al. – Biochemistry

Pregnancy and early life

Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin – Richard G. Brown et al. – BMC Medicine

Human skin microbiome

* Review: Skin microbiota–host interactions – Y. Erin Chen et al. – Nature

Human vaginal microbiome

Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim and Yoo Jin Park – Journal of Menopausal Medicine

Human oral microbiome

Silver Fluoride as a Treatment for Dental Caries – J.A. Horst – Advances in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu & Z. Ren et al. – Advances in Dental Research

Video protocol: Oral Biofilm Sampling for Microbiome Analysis in Healthy Children – Elisabeth Santigli et al. – JoVE

Human gut microbiome

Review: Clostridium difficile control measures: current and future methods for prevention – Erik R. Dubberke & Carlos Mejia-Chew – Expert Review of Anti-infective Therapy

Review: Colorectal Cancers: An Update on Their Molecular Pathology – Kentaro Inamura – Cancers

Review: Role of microbiota-derived lipopolysaccharide in adipose tissue inflammation, adipocyte size and pyroptosis during obesity – Lars-Georg Hersoug et al. – Nutrition Research Reviews

* Review: Role of priority effects in the early-life assembly of the gut microbiota – Daniel Sprockett et al. – Nature Reviews Gastroenterology & Hepatology

Review: Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes – Candice Colbey et al. – Sports Medicine

Review: Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems – R. J. Mulders et al. – Obesity Reviews

Factors Associated with the Use of Fecal Microbiota Transplant in Patients with Recurrent Clostridium difficile Infections – Sehrish Jamot et al. – Infection Control & Hospital Epidemiology

Animal experiments

Zebrafish: Dysregulation of Intestinal Health by Environmental Pollutants: Involvement of the Estrogen Receptor and Aryl Hydrocarbon Receptor – Lianguo Chen et al. – Environmental Science & Technology

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice – Feifei Lin et al. – Food & Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista et al. – British Journal of Nutrition

Rat: Berberine Modulates Gut Microbiota and Reduces Insulin Resistance via the TLR4 Signaling Pathway – Dan Liu & Yiyi Zhang et al. – Experimental and Clinical Endocrinology & Diabetes

Early microbial colonization affects DNA methylation of genes related to intestinal immunity and metabolism in preterm pigs – Xiaoyu Pan et al. – DNA Research

Mouse: Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism – Kairui Mao et al. – Nature

* Influence of excessive exercise on immunity, metabolism and gut microbial diversity in an overtraining mice model – Xin Yuan et al. – Scandinavian Journal of Medicine & Science in Sports

* Mouse: An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin et al. – Genome Biology

* Gut Microbiota-Derived Short Chain Fatty Acids Induce Circadian Clock Entrainment in Mouse Peripheral Tissue – Yu Tahara et al. – Scientific Reports

Time-course responses of ileal and fecal microbiota and metabolite profiles to antibiotics in cannulated pigs – Kan Gao et al. – Applied Microbiology and Biotechnology

Preprint: Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A Hatter et al. – bioRxiv

Animal microbiome

Rapid and Specific Methods to Differentiate Foodborne Pathogens, Campylobacter jejuni, Campylobacter coli, and the New Species Causing Spotty Liver Disease in Chickens, Campylobacter hepaticus – Thi Thu Hao Van et al. – Foodborne Pathogens and Disease

Microbial community and short-chain fatty acid profile in gastrointestinal tract of goose – H Yang et al. – Poultry Science

Exploration of the faecal microbiota and biomarker discovery in equine grass sickness – Joy Leng et al. – Journal of Proteome Research

Plant, root and soil microbiome

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad et al. – Environmental Science & Technology

Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata et al. – Letters in Applied Microbiology

Opinion piece: Plant pathogen effector proteins as manipulators of host microbiomes? – Nick C. Snelders et al. – Molecular Plant Pathology

Water and extremophile microbiome

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity – David Lopez-Escardo et al. – bioRxiv

Food microbiome

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes – Yuanchen Zhang et al. – Nature Communications

Phages and viruses

Distinct Effects of Type I and III Interferons on Enteric Viruses – Harshad Ingle et al. – Viruses

Technology

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving et al. – Clinical Metabolomics

NMR Analysis of Fecal Samples – Hye Kyong Kim et al. – Clinical Metabolomics

Bioinformatics

Spherical: an iterative workflow for assembling metagenomic datasets – Thomas C. A. Hitch and Christopher J. Creevey – BMC Bioinformatics

Microbes in the news

Middle Eastern diet increases gut microbiota diversity, shows benefit in cirrhosis – Healio

Bacterial DNA sequencing could help design ‘friendlier’ nanoparticles – Belle Dumé – Nanotechweb

Consumption of Dietary Fiber May Prevent Metabolic Syndrome – Anamika P – TGHN

Researchers Discover 10 New Immune Systems in Bacteria – Jim Daley – The Scientist

New Ocean-Dwelling, Bacteria-Killing Tailless Virus Hid in Plain Sight – Mindy Weisberger – Live Science

New method developed to detect bacteria in food and water – Ananya Mandal – News Medical

eNose Successfully Recognizes Bacteria in Common Soft Tissue Infections – Michaela Fleming – Contagion Live

Are There Zombie Viruses In The Thawing Permafrost? – Michaeleen Doucleff – NPR

* ‘He was so strong’: Boy, 8, dies from flesh-eating bacteria – by Associated Press – New York Post

Publishing and education

Preprint: Harmonizing semantic annotations for computational models in biology – Maxwell L Neal et al. – bioRxiv

January 25, 2018

Posted on January 25, 2018 by barnettburns

Female sexual and reproductive microbiome: A Bayesian network of the relationship between the vaginal microbiome, habits, demographics and infection risk in reproductive age women, a new mouse model of HIV co-infection demonstrates increased viral shedding in the vagina after gonorrhoeae bacterial infection, and the impacts of diet-induced obesity during pregnancy on the maternal metabolome and gene expression in the placenta in mice.

Water microbiome: How urbanization impact coastal microbiomes, as well as novel organisms from Baltic Sea sediment, and deep-sea hydrothermal vents.

Events and jobs

Clinical Lab Technical Asst Sr – Scripps Health – San Diego CA

Postdoctoral Associate in Soil Health and Water Quality – Stroud Water Research Center – Southeast Pennsylvania

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Human oral microbiome

Review: Salivary biomarkers for oral cancer and pre-cancer screening: a review – J Kaur – Clinical Oral Investigations

Review: In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P.D. Marsh – Advanced in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu – Advanced in Dental Reserach

Human vaginal microbiome

Review: Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim – Journal of Menopausal Medicine

*Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis – Noelle Noyes – PLOSone

Human gut microbiome

Review: Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Review: Microbiome: Gut microbiota sways response to cancer immunotherapy – Ashley York – Nature Reviews Microbiology

Review: Bacterial Signaling at the Intestinal Epithelial Interface in Inflammation and Cancer – Olivia I. Coleman

Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis – Tsuyoshi Sekizuka – PLOSone

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Animal experiments

*Diet-induced obesity alters the maternal metabolome and early placenta transcriptome and decreases placenta vascularity in the mouse – Tami J Stuart – Biology of Reproduction

Gastrointestinal Tract Pathology in a BALB/c Niemann–Pick Disease Type C1 Null Mouse Model – Antony Cougnoux – Digestive Diseases and Sciences

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice – Feifei Lin – Food and Function

*Neisseria gonorrhoeae co-infection exacerbates vaginal HIV shedding without affecting systemic viral loads in human CD34+ engrafted mice – Stacey X. Xu – PLOSone

Plant, root, and soil microbiome

Interspecific plant interactions reflected in soil bacterial community structure and nitrogen cycling in primary succession – Joseph E. Knelman – Frontiers in Microbiology

Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing – Zhang Wei – Archives of Microbiology

Rhizosphere competence and biocontrol effect of Pseudomonas sp. RU47 independent from plant species and soil type at the field scale – Susanne Schreiter – Frontiers in Microbiology

Estimation of throughfall and stemflow bacterial flux in a subtropical oak-cedar forest – Thais B. Bittar – Geophysical Research Letters

NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards – Nikoletta Czotter – Frontiers in Microbiology

Microbial Remediation of Heavy Metals and Arsenic-Contaminated Environments in the Arid Zone of Northwest China – Xiangliang Pan – In: Luo Y., Tu C. (eds) Twenty Years of Research and Development on Soil Pollution and Remediation in China. Springer, Singapore

Review: Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata – Letters in Applied Microbiology

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad – Environmental Science and Technology

Water and extremophile microbiome

*Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea – Verona Vandieken – Frontiers in Microbiology

*Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

*Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen – Nicole Adam – The ISME Journal

The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary – Timothy G. Otten – Environmental Microbiology

Built environment

Dissertation: Developing Quantitative Abundance Metrics for Microbial Communities – Gabriel Goodney – San Diego State University

Resistome

Antibiotic resistance mutations induced in growing cells of Bacillus-related thermophiles – Hirokazu Suzuki – The Journal of Antibiotics

Food microbiology

A metabolomics study reveals enhanced inhibition and metabolic dysregulation in E. coli induced by Lactobacillus acidophilus fermented black tea extract – Kundi Yang – Journal of Agricultural and Food Chemistry

More Microbes

Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free-living Giant Amoebae – Georgia M. Ward – Eukaryotic Microbiology

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Phages and viruses

Rolling-circle replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases of the IS91 family insertion sequences – Yuchen Wang – Journal of General Virology

Preprint: Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – Bob G. Blasdel – BioRxiv

Bioinformatics

Phylogeny-Based Kernels with Application to Microbiome Association Studies – Jian Xiao – New Advances in Statistics and Data Science

Techniques

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities – Fabien Cottier – npj Biofilms and Microbiomes

Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry – Zishu Liu – mSphere

Deconvolution models for a better understanding of natural microbial communities enumerated by flow-cytometry – Gianluca Corno – Cytometry

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Microbes in the news

Bacteria could cause women to give birth prematurely, study finds – Sabrina Barr – Independent

PCOS may reduce gut bacteria diversity – EurekAlert!

Root microbiome valuable key to plants surviving drought – Elaine Smith – Phys.org

Studies in Mice Suggest How Dietary Fiber Reduces Harmful Effects of High-Fat Diet – Genetic Engineering and Biotechnology News

Helicobacter pylori infection permanently changes gastric environment – Medical Press

Dietary Fiber Intake Protects against Diet-Induced Obesity and Metabolic Syndrome – SCI News

The Microbiome of an Oil Reservoir – UC San Diego

Mucin Cross-Feeding Shapes The Metabolic Environment In The Infant Gut – Vera Bunesova – Science Trends

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin – Genome Biology

January 24, 2018

Posted on January 24, 2018 by edwardmessick

General microbiome

Meta-analysis generates and prioritizes hypotheses for translational microbiome research – Claire Duvallet – microbial biotechnology

Resistance to Antibiotics: Are we prepared to Handle This Growing Ghost? – Ashima Kushwaha Bhardwaj – Omics Ebook Group

Pregnancy and early life

Neonate gut and respiratory microbiota: coordinated development through time and space – Alex Grier – bioRxiv

Human oral microbiome

Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications – A. Mira – Advances in Dental Research (SAGE Journals)

Rebalancing the Caries Microbiome Dysbiosis: Targeted Treatment and Sugar Alcohols – L. Zhan – Advances in Dental Research (SAGE Journals)

The Caries Microbiome: Implications for Reversing Dysbiosis – A.C.R. Tanner – Advances in Dental Research (SAGE Journals)

In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P. D. Marsh – Advances in Dental Research (SAGE Journals)

Getting to Know “The Known Unknowns”: Heterogeneity in the Oral Microbiome – R. A. Burne – Advances in Dental Research (SAGE Journals)

Human gut microbiome

Adaptive Immune Education by Gut Microbiota Antigens – Qing Zhao – Immunology

Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Characterization of the fecal microbiota differs between age groups in Koreans – Sun-Young Kook – Intestinal Research

Diet, microbiota and inflammatory bowel disease: review – Bruna Luísa Radavelli – Nutrition & Food Science

The Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pylori – Ingeborg Klymiuk – Frontiers in Microbiology

Gut Microbial Diversity in Women with Polycystic Ovary Syndrome Correlates with Hyperandrogenism – Pedro J Torres – JCEM

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Celiac Disease Patients and Controls – Sudarshan A Shetty – bioRxiv

Animal experiments

Modeling Host-Microbiome Interactions in Caenorhabditis elegans – Teklu K. Gerbaba – Journal of Nematology

The anti-inflammatory IFITM genes ameliorate colitis and partially protect from tumorigenesis by changing immunity and microbiota – Zoya Alteber – Immunology & Cell Biology

A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols – Mei Cheng – Food & Function

Animal microbiome

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica – Juan G. Abarca – Frontiers in Microbiology

Functional Characteristics of the Flying Squirrel’s Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling – Hsiao-Pei Lu – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

Out of sight, but no longer out of mind – towards an increased recognition of the role of soil microbes in plant speciation – József Geml – New Phytologist

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

Assembly and ecological function of the root microbiome across angiosperm plant species – Connor R. Fitzpatrick – PNAS

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome – Jaderson Silveira Leite Armanhi – Frontiers in Plant Science

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function – Baneshwar Singh – Frontiers in Microbiology

Water and extremophile microbiome

Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation – Peike Gao – Applied Microbiology and Biotechnology

Evidence for Coupling of the Carbon and Phosphorus Biogeochemical Cycles in Freshwater Microbial Communities – O Roger Anderson – Frontier in Marine Science

Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields – Teresa Cerqueira – Environmental Microbiology

Bioinformatics

Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems – Ángel Martín Ortiz-Estrada – Reviews in Agriculture

[MSc Thesis] Optimizing the Reconstruction of Microbial Population Genomes from Metagenomes – Bhavya Nalagampalli Papudeshi – San Diego State University, ProQuest Dissertations Publishing

Extension of the viral ecology in humans using viral profile hidden Markov models – Zurab Bzhalava – PLOS One

Metataxonomic approach to decipher the polymicrobial burden in diabetic foot ulcer and its biofilm mode of infection – Karthika Suryaletha – International Wound Journal

A strategy for association study on intestinal microbiome and brain metabolome across lifespan of rats – Tianlu Chen – Analytical Chemistry

Techniques

The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows – Jueeli D. Vaidya – Frontiers in Microbiology

Microbes in the news

Hyperandrogenism may alter gut microbiome in PCOS

Ed’s non-microbiology picks

Using Fungi to Fix Bridges

Cooperating with machines – Jacob W. Crandall – Nature Communications

An investigation into the nutritional composition and cost of gluten-free versus regular food products in the UK – L. Fry – Journal of Human Nutrition and Dietetics

Prevalence and Trends in Prepregnancy Normal Weight — 48 States, New York City, and District of Columbia, 2011–2015 – CDC / Morbidity and Mortality Weekly Report

Exposed subsurface ice sheets in the Martian mid-latitudes – Colin M. Dundas – Science

Shorter sleep duration and longer sleep onset latency are related to difficulty disengaging attention from negative emotional images in individuals with elevated transdiagnostic repetitive negative thinking – Jacob A. Nota – Journal of Behavior Therapy and Experimental Psychiatry

January 23, 2018

Posted on January 23, 2018 by xinhuang7

After the US government shutdown, today’s Digest features several human gut microbiome, food microbiology papers and many news pieces. There are some other highlights as well. A large longitudinal experiment in a tropical rain forest examines how soil microbes adapt genetically to nutrient changes in the soil. A synthetic enzyme rescues E. coli in iron-limited medium. Open access from high impact medical journals is still lacking.

Jobs and events

Digital Communications Officer – Microbiology Society – London

Keystone Symposium on Natural Products and Synthetic Biology

General microbiology

Sequence-based classification and identification of Fungi – David Hibbett et al. – Mycologia

Preprint: E. coli translation strategies differ across nutrient conditions – Sophia Hsin-Jung Li et al. – bioRxiv

* A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli – Ann E Donnelly et al. – Nature Chemical Biology

Press: A randomly generated, totally novel enzyme rescues mutant bacteria – Diana Gitig – ArsTechnica

Annotations of Microbacterium foliorum – Debbie Jacobs-Sera – Sea Phages

Human gut microbiome

Reoccurring review (no abstract available): Letter to the Editor: Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Andre Alonso Taco-Masias and Augusto Rafael Fernandez-Aristi – Obesity Surgery

Also see a previous review: Influence of intestinal microbiota on body weight gain: a narrative review of the literature – Camila S. Cardinelli et al. – Obesity Surgery

Impact of intestinal mannitol on hyperammonemia, oxidative stress and severity of hepatic encephalopathy in the ED – Daniel H. Montes-Cortés et al. – The American Journal of Emergency Medicine

Clostridial strain-specific characteristics associated with necrotizing enterocolitis – Sophia Schönherr-Hellec et al. – Applied and Environmental Microbiology

Intestinal dysbiosis and permeability: the yin and yang in alcohol dependence and alcoholic liver disease – Peter Stärkel et al. – Clinical Science

In vitro fermentation of Cookeina speciosa glucans stimulates the growth of the butyrogenic Clostridium cluster XIVa in a targeted way – Thaisa MoroCantu-Jungles et al. – Carbohydrate Polymers

Animal microbiome

In vitro: Rumen bacteria at work: bioaugmentation strategies to enhance biogas production from cow manure – E.G. Ozbayram et al. – Journal of Applied Microbiology

Plant, root and soil microbiome

* Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil – Qiuming Yao et al. – Nature Ecology and Evolution

Press: Researchers reveal how microbes cope in phosphorus-deficient tropical soil – Sara Shoemaker – Phys.org

Water and extremophile microbiome

Bacterial community changes in copper and PEX drinking water pipeline biofilms under extra disinfection and magnetic water treatment – J. Inkinen et al. – Journal of Applied Microbiology

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber – M. Salomez et al. – Journal of Applied Microbiology

Lead-resistant bacteria from Saint Clair River sediments and Pb removal in aqueous solutions – Nichole Bowman et al. – Applied Microbiology and Biotechnology

Food microbiology

Ultrasound improves antimicrobial effect of sodium dichloroisocyanurate to reduce Salmonella Typhimurium on purple cabbage – Ana Lúcia Almeida Duarte et al – International Journal of Food Microbiology

Characterization of the spoilage potential of pure and mixed cultures of bacterial species isolated from tropical yellowfin tuna (Thunnus albacares) – A. Silbande et al. – Journal of Applied Microbiology

Impact of storage conditions on fungal community composition of green coffee beans Coffea arabica L. stored in jute sacks during 1 year – L.M. Broissin-Vargas et al. – Journal of Applied Microbiology

An assessment of the microbiological quality and safety of raw drinking milk on retail sale in England – C. Willis et al. – Journal of Applied Microbiology

Microbes in the news

Bacteria warning for Kapiti waterways – Newshub

Common salt kills rat fever bacteria? Public health experts say it can – TNN – Times of India

Editorial: Vendors’ ultimatum will save us from cholera, typhoid – The Standard

Why Flesh-Eating Bacteria Can Look Like the Flu – Rachael Rettner – Live Science

Geologists find bacteria that takes traces of gold and turns them into nuggets – Eliza Goetze – ABC News

Shigella Bacteria Diarrhea in Children: Should WHO Guidelines Be Modified? – Julie McShane – Medical News Bulletin

* Chemical ‘aphrodisiac’ jumpstarts the sex life of a single-celled organism – Brianna Abbott – Science Line

Microbiome predicts blood infections in pediatric cancer patients – EurekAlert

Dietary Fiber Protects Against Obesity and Metabolic Syndrome, Study Finds – Georgia State University News Hub

How climate change weakens coral ‘immune systems’ – EurekAlert

* Early changes in brain immunity may underlie sex bias in autism – Nicholette Zeliadt – Spectrum

Detecting Zoonotic Protists In Raw Sewage For Environmental Monitoring – Steven Sullivan – Science Trends

Microbes on the market

Synspira Therapy Eliminates Antibiotic-resistant Lung Bacteria, Study Shows – Marta Figueiredo – Cystic Fibrosis News Today

Microbiome Sequencing Service Market – Baseclear, Clinical-Microbiomics, MR DNA (Molecular Research Lp), Molzym, Zymo Research, Rancho Biosciences, Microbiome Therapeutics, Microbiome Insights, Openbiome, Resphera Biosciences, Shanghai Realbio Technology – Oscar – Hugo Press

VALBIOTIS Announces a Significant Effect of VALEDIA® on Intestinal Microbiota – Business Wire

Publishing and education

* Preprint: Open access policies of high impact medical journals: a cross-sectional study – Time Ellison et al. – bioRxiv

January 22, 2018

Posted on January 22, 2018 by TinaS

Quite a short digest today, still many interesting articles. Today I would like to focus on two papers, both related to water microbiome. In the first one Antonio M. Martin-Platero et al. show how microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp, while the paper by Yoann Seeleuthner et al. reveals underestimated functional diversity of uncultured marine protists across oceans. The third paper I would like to mention is a report by Manuel Delgado-Baquerizo, which provides a global atlas of the dominant bacteria found in soil.

Jobs

Research Technician, Newcastle University, UK

Research Technician (Microbiology & Microbial Genetics), Newcastle University, UK

Postdoc position in the Antimicrobial Resistance Unit, University Complutense of Madrid – UCM, Madrid, Spain

General microbiome

E. coli translation strategies differ across nutrient conditions – Sophia Hsin-Jung Li – bioRxiv

Oral microbiome

Clinical and microbiological evaluation of the effect of Lactobacillus reuteri in the treatment of mucositis and peri-implantitis: A triple-blind randomized clinical trial – M. Galofré – Journal of periodontal research

Human gut microbiome

Intestinal Epithelial Cell–Derived LKB1 Suppresses Colitogenic Microbiota – Xia’nan Liu – The Journal of Immunology

Microbial regulation of the L cell transcriptome – Tulika Arora – Scientific Reports

Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study – Yang Shen – Schizophrenia Research

1-Day or 5-Day Fecal Samples, Which One is More Beneficial to be Used for DNA-Based Gut Microbiota Study – Tingting Su – Current Microbiology

16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones – Ruiqiang TangYonghua Jiang – Urolithiasis

Structural characterization and in vitro fermentation of a novel polysaccharide from Sargassum thunbergii and its impact on gut microbiota – Xiong Fu – Carbohydrate Polymers

Oral Administration of Compound Probiotics Ameliorates HFD-Induced Gut Microbe Dysbiosis and Chronic Metabolic Inflammation via the G Protein-Coupled Receptor 43 in Non-alcoholic Fatty Liver Disease Rats – Yinji Liang – Probiotics and Antimicrobial Proteins

Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases – Rachel Fellows – Nature Communications

Plant, root, and soil microbiome

Report: A global atlas of the dominant bacteria found in soil – Manuel Delgado-Baquerizo – Science

Water and extremophile microbiome

Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River – Tang Liu – BMC Microbiome

Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments – M.del R.Mora-Ruiz – Systematic and Applied Microbiology

High resolution time series reveals cohesive but short-lived communities in coastal plankton – Antonio M. Martin-Platero – Nature Communication

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans – Yoann Seeleuthner – Nature Communications

Microbes in the news

New type of steel kills bacteria with … nanoparticles!

The Prehistoric Bacteria That Helped Create Our Cells Billions of Years Ago

January 21, 2018

Posted on January 21, 2018 by Kiran

A light reading for Sunday!

Events and jobs

Professor (Chairperson), Department of Microbiology and Immunology (MIC) – The Uniformed Services University of the Health Sciences – Bethesda, Maryland

Postdoc in Intestinal Microbiology and Ecology – The National Food Institute (DTU Food) – Denmark

SCIENCE INQUIRY LECTURE: “FLYING” BACTERIA AS POTENTIAL RAINMAKERS – APRIL 18, 2018; 7:00PM – 8:30PM – HAGER AUDITORIUM, Montana

General microbiome

Review: Bacterial RNA Biology on a Genome Scale – Jens Hör – Molecular Cell

Multi-site human microbiome

Epigenetics, microbiota, and intraocular inflammation: New paradigms of immune regulation in the eye – Xiaofeng Wen – Progress in Retinal and Eye Research

Human skin microbiome

The role of fatty acids and their endocannabinoid-like derivatives in the molecular regulation of appetite – Renger F. Witkamp – Molecular Aspects of Medicine

Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair – Jonathan L. Linehan – Cell

Propionibacterium acnes Strains Differentially Regulate the Fate of Th17 Responses in the Skin – Emmanuel Contassot – Journal of Investigative Dermatology

Human gut microbiome

P038 FECAL MICROBIOTA TRANSPLANT (FMT) FOR IMMUNO-CHECKPOINT INHIBITOR-INDUCED COLITIS (ICI-C) IN A 50 YEAR OLD FEMALE WITH BLADDER CANCER – Yinghong Wang – Gastroenterology

P110 STEROID-RESISTANCE AND STEROID-DEPENDENCE IN INFLAMMATORY BOWEL DISEASE CAN BE LINKED WITH GUT MICROBIOTA COMPOSITION CHANGES – Natalia Danilova – Gastroenterology

P069 LOW FAT DIET IMPROVES QUALITY OF LIFE AND CHANGES THE MICROBIOME IN A CATERED, CROSS-OVER DESIGN INTERVENTION OF UC PATIENTS WITH QUIESCENT DISEASE: RESULTS OF A PILOT STUDY – Matthew C. Phillips – Gastroenterology

Animal experiments

The family Coriobacteriaceae is a potential contributor to the beneficial effects of Roux-en-Y gastric bypass on type 2 diabetes – Haijun Liu – Surgery for Obesity and Related Diseases

P039 FECAL MIRNAS SHAPE THE INTESTINAL MICROBIOTA – Emilie Viennois – Gastroenterology

P125 TLR4 ACTIVATION UPREGULATES EXPRESSION OF OXIDATIVE ENZYMES: IMPLICATIONS FOR INTESTINAL TUMORIGENESIS AND LUMINAL MICROBIOTA – Juan F. Burgueno – Gastroenterology

Effect of live yeast supplementation on gastric ecosystem in horses fed a high-starch diet – Samy Julliand – Livestock Science

The symbiont Lactobacillus plantarum causes intestinal pathogenesis in adult Drosophila. – David Fast – bioRxiv

Plant, root and soil microbiome

Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation – Chao Ai – Geoderma

Microbial degradation of poly(ε-caprolactone) in a coastal environment – Miwa Suzuki – Polymer Degradation and Stability

Shifts in prokaryotic communities under forest and grassland within a tropical mosaic landscape – Sergio E. Morales – Applied Soil Ecology

Food microbiology

Polyphasic identification of Penicillia and Aspergilli isolated from Italian grana cheese – Simone Decontardi – Food Microbiology

Phages and viruses

Bacteriophages as modulator for the human gut microbiota: Release from dairy food systems and survival in a dynamic human gastrointestinal model – Meike Samtlebe – LWT

Techniques

Metagenomic analysis uncovers strong relationship between periodontal pathogens and vascular dysfunction in American Indian population – Prathik K Vijay Kumar – bioRxiv

P168 WHERE WILL FECAL MICROBIOTA TRANSPLANTATION FIT IN THE TREATMENT ALGORITHMS FOR CROHN’S DISEASE AND ULCERATIVE COLITIS: A SYNTHESIS OF COMPLETED, ONGOING AND FUTURE TRIALS – Yiran Song – Gastroenterology

Microbes in the news

The Prehistoric Bacteria That Helped Create Our Cells Billions of Years Ago – Mental Floss

IIT Delhi develops a novel platform to test drug sensitivity in bacteria – The Hindu

Scientists Unlock Key Information About the World’s Soil Microbes – Yale Environment 360

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A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

General microbiome

Multi-site human microbiome

Human respiratory microbiome

Human skin microbiome

Human vaginal microbiome

Human gut microbiome

Animal experiments

Animal microbiome

Plant, root and soil microbiome

Water microbiome and extremophiles

Food microbiology

Phages and viruses

Techniques

Microbes in the news

A Saturday digest with lots of fun and weird news of microbiome!

Events and jobs

General microbiome

Pregnancy and early life

Human gut microbiome

Animal experiments

Plant, root and soil microbiome

Water microbiome and extremophile

Food microbiology

Phages and viruses

Microbes in the news

A light reading for Sunday!

Events and jobs

General microbiome

Multi-site human microbiome

Human skin microbiome

Human gut microbiome

Animal experiments

Plant, root and soil microbiome

Food microbiology

Phages and viruses

Techniques

Microbes in the news