Category Archives: Human oral

November 8, 2016

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I’m sick at home but my inbox is exploding with new papers, so I scraped myself together for a new Microbiome Digest.

Precision medicine and the microbiome, salivary microbiome of Tsimane mothers and infants, food emulsifiers promote colon cancer in mice, microplastics in urban rivers, and a hypothetical silver Nobel prize for Jeffrey Gordon.

Events

SF Bay Area Microbiome meetup – a new LinkedIn group for people in the San Francisco area interested in all things microbiome!

Society of Nutrition Education and Behavior (SNEB) Webinar – Probiotics: Understanding The Microbiome And The Role Of Probiotics In Long Term Health – Wednesday, December 7 at 12:00 p.m. EST

This one is about me: Stanford Microbiome Pioneer Elisabeth Bik Becomes New Science Editor at uBiome – uBiome

General microbiome

Introducing the Microbiome into Precision Medicine – Thomas M. Kuntz, Jack A. Gilbert – Trends in Pharmacological Sciences

Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche – Sarah M. Kopac – Frontiers in Microbiology

Opinion: Do antibodies select a healthy microbiota? – Jason L. Kubinak & June L. Round – Nature Reviews Immunology

Editorial: Complexity at the sub-genus level – Andrea Du Toit – Nature Reviews Microbiology

Human oral microbiome

Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication – Cliff S. Han – PeerJ

A Pilot Study to Evaluate the Oral Microbiome and Dental Health in Primary Open-Angle Glaucoma – Polla, Daniel – Journal of Glaucoma

Sputum microbiology predicts health status in COPD – DCW Braeken – International Journal of Chronic Obstructive Pulmonary Disease

Human respiratory microbiome

Assessing the Airway Microbiota in Cystic Fibrosis – Jordana E. Hoppe – Clinical Microbiology Newsletter

Review: The microbiome-metabolome crosstalk in the pathogenesis of respiratory fungal diseases – Samuel M. Gonçalves – Virulence

Human vaginal microbiome

Effects of pelvic organ prolapse ring pessary therapy on intravaginal microbial flora – Kazuaki Yoshimura – International Urogynecology Journal

Review: Why do lactobacilli dominate the human vaginal microbiota? – SS Witkin – BJOG

Human gastric microbiome

Characterization of the Gastric Microbiota in a Pediatric Population According to Helicobacter pylori Status – Llorca, Laura – The Pediatric Infectious Disease Journal

Human gut microbiome

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome – Hailiang Xie – Cell Systems

Culture of previously uncultured members of the human gut microbiota by culturomics – Jean-Christophe Lagier – Nature Microbiology

Impact of Cystic Fibrosis Disease on Archaea and Bacteria Composition of Gut Microbiota – Francesco Miragoli – FEMS Microbiology Ecology

Animal models

Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota
– Matthew B Biggs – The ISME Journal

Gut microbiota induce IGF-1 and promote bone formation and growth – Jing Yan – PNAS

Dietary emulsifier-induced low-grade inflammation promotes colon carcinogenesis – Emilie Viennois – Cancer Research

Chronic Opisthorchis viverrini Infection Changes the Liver Microbiome and Promotes Helicobacter Growth – Upsornsawan Itthitaetrakool – PLOS ONE

Sex-specific modulation of the gut microbiome and behavior in Siberian hamsters – Kristyn E. Sylvia – Brain, Behavior, and Immunity

Animal microbiome

Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates – Julie C. McInnes – Methods in Ecology and Evolution

High-throughput sequencing highlights the significant influence of seasonal housing and teat preparation on the raw milk microbiota – Conor J Doyle – Applied and Environmental Microbiology

Metagenomic analysis reveals the influences of milk containing antibiotics on the rumen microbes of calves – Wei Li – Archives of Microbiology

Repeated sampling of white syndrome-affected corals reveals distinct microbiome at disease lesion fronts – F. Joseph Pollock – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Relationships between soil fungal and woody plant assemblages differ between ridge and valley habitats in a subtropical mountain forest – Cheng Gao – New Phytologist

AMF, phylogeny, and succession: specificity of response to mycorrhizal fungi increases for late-successional plants – Liz Koziol – Ecosphere

Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils – William A. Argiroff – Microbial Ecology

Effect of disturbance by oil pollution on the diversity and activity of bacterial communities in biological soil crusts from the Sultanate of Oman – Raeid M.M. Abed – Applied Soil Ecology

Book chapter: Root-Microbe Interactions in Response to Soil Conditions – Anil Somenahally – Global Soil Security

Water and extremophile microbiome

Microplastic in surface waters of urban rivers: concentration, sources, and associated bacterial assemblages – Amanda R. McCormick – Ecosphere

Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii – Jason B. Sylvan – Geochimica et Cosmochimica Acta

Bacterial metacommunity organization in a highly-connected aquatic system – Silke Langenheder – FEMS Microbial Ecology

Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland – Malin Bomberg – Biogeosciences

Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia
– Shipeng Lu – Environmental Microbiology Reports

Review: Microbial Community Assessment in Wetlands for Water Pollution Control: Past, Present, and Future Outlook – Kela P. Weber – Water

Bioinformatics and metagenomics

Alternative for PiCRUST: Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes – Shoko Iwai – PLOS ONE

Measurement of bacterial replication rates in microbial communities – Christopher T Brown – Nature Biotechnology

Microbes in the news

If there was a Nobel silver medal, I’d award it to Jeffrey Gordon and our gut microbes – Tim Spector – The Conversation

The Microbiome Hits #1 for 2017: Cleveland Clinic’s announcement of the Top 10 Medical Innovations came at the conclusion of the 2016 Medical Innovation Summit.

Gut Instincts: The Link Between Diet, the Gut Microbiota and the Brain – Kiana West – Imperial College London

Q&A with Stanford statistics Professor Susan Holmes: Statistics in the era of big data – Stanford News

Conference report: Gut microbes linked to immunotherapy response in melanoma patients – EurekAlert

Gut bacteria ‘may help drugs fight cancer’ – James Gallagher – BBC

Assistant professor Joanna Slusky recognized for work with antibiotic-resistant bacteria – The University Daily Kansan

Three Soundcloud episodes by the Yale Journal of Biology and Medicine on the microbiome, to accompany their September issue:

  1. Microbiome: Episode I: history of the field, current techniques used in microbiome research, and how the microbiome influences our health
  2. Microbiome: Episode IIMicrobiome: Episode II: Dr. Martin Kriegel discusses articles published in our issue, – Yale Journal of Biology and Medicine
  3. Microbiome: Episode III: Dr. Camille Konopnicki, talks about current on going research on the microbiome here at Yale and how microbiome research is evolving and changing.

Companies Bet on Designer Bacteria as New Way to Treat Disease – MIT Technology Review

About Bethany Rader: Researcher studying squid-human bacteria connection – Tim Crosby – The Southern Illinoisan

Horrible title, but nice student work: Students create Frankenstein’s monster of bacteria to detect toxic chemicals – New Atlas

 

October 27, 2016

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Kavli Foundation grants, mycobiome of root canal infections, post-stroke infections,  Thai vegetarians, antibiotic treatment of gorillas, licorice plants under salt stress, and bacterial camouflage on Crustaceans. Greetings from New Mexico!

Jobs and grants

Open Positions at NC State University: Microbiomes and Complex Microbial Communities

Uniting Diverse Sciences to Tackle the Microbiome – Kavli Foundation

Human oral microbiome

The mycobiome of root canal infections is correlated to the bacteriome – Ilona F. Persoon – Clinical Oral Investigations

Near-sterile human body sites

Comprehensive detection and identification of bacterial DNA in the blood of patients with sepsis and healthy volunteers using next-generation sequencing method – the observation of DNAemia – T. Gosiewski – European Journal of Clinical Microbiology & Infectious Diseases

Human respiratory microbiome

Translocation and dissemination of commensal bacteria in post-stroke infection – Dragana Stanley – Nature Medicine

Bacteria in the respiratory tract—how to treat? Or do not treat? – Cristina Prat – International Journal of Infectious Diseases

Human gut microbiome

Human Microbiome Fusobacterium Nucleatum in Esophageal Cancer Tissue Is Associated with Prognosis – Kensuke Yamamura – Clinical Cancer Research

Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk – Supatjaree Ruengsomwong – Journal of Microbiology and Biotechnology

Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study – Andrea Quagliariello – Nutrients

Review: Rethinking Diet to Aid Human–Microbe Symbiosis – Muriel Derrien – Trends in Microbiology

Review: Feeding the Microbiota-Gut-Brain Axis: Diet, Microbiome and Neuropsychiatry – Kiran V. Sandhu – Translational Research

Review: Microbiota dysbiosis: a new piece in the understanding of carcinogenesis puzzle – Valeria García-Castillo – Journal of Medical Microbiology

Review: The evolving role of the microbiome in liver failure and liver transplantation – Kymberly D. Watt – Liver Transplantation

Animal models

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla) – Klára Vlčková – Microbial Ecology

Commensal Microbe-specific Activation of B2 Cell Subsets Contributes to Atherosclerosis Development Independently of Lipid Metabolism – Lin Chen – EBioMedicine

Commentary: Intestinal Microbiome and Atherosclerosis – J. David Spence – EBioMedicine

A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model – Susanne C. Diesner – Clinical Immunology

Kinetic changes of intestinal microbiota in the course of intestinal sensitization – Liang Xiao – Oncotarget

Animal microbiome

Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts – Gwynneth F. Matcher – Microbiology Open

Plant, root, and soil microbiome

Divergent responses of β-diversity among organism groups to a strong environmental gradient – Micael Jonsson – Ecosphere

Phylogenetic congruence between subtropical trees and their associated fungi – Xubing Liu – Ecology and Evolution

Microbial cooperation in the rhizosphere improves liquorice growth under salt stress – Dilfuza Egamberdieva – Bioengineered

Extremophile microbiome

Extremophiles: Life at the deep end – Sonja-Verena Albers – Nature

Built environment microbiome

Dynamic change of surface microbiota with different environmental cleaning methods between two wards in a hospital – Applied Microbiology and Biotechnology

Bioreactor microbiology

In vitro study of soil arsenic release by human gut microbiota and its intestinal absorption by Caco-2 cells – Naiyi Yin – Chemosphere

Probiotics

Probiotic With or Without Fiber Controls Body Fat Mass, Associated With Serum Zonulin, in Overweight and Obese Adults—Randomized Controlled Trial  – Lotta K. Stenman – EBioMedicine

More microbes

Nanostructures and Monolayers of Spheres Reduce Surface Reflections in Hyperiid Amphipods – Laura E. Bagge – Current Biology

Press: Crustaceans in the ocean’s ‘twilight zone’ wear CAMOUFLAGE: Bacteria coating helps creatures avoid a predator’s gaze – Sarah Griffiths – Daily Mail

Microbes in the news

Videos from Microbiomes of the Built Environment NAS meeting posted – Jonathan Eisen – MicroBEnet

Iron-Loving Bacteria a Model For Mars Life – Elizabeth Howel –  Space.com

Dogs go on poop patrol to sniff out fecal bacteria. Rescue dogs trained to detect human fecal matter – Barbara Besteni – Local 10

Bacteria Sent In Space Could Be Potentially Infectious, Harmful – Elaine Hannah – Science World Report

Florida’s orange groves are being wiped out by tree-killing bacteria – CBS News

Rio fights Zika with biggest release yet of bacteria-infected mosquitoes. Wolbachia-infected mosquitoes will be widely deployed in two South American cities to combat viral infections – Ewen Callaway – Nature

Cranberries crush bacteria’s communication networks – Lisa-Ann Lee – New Atlas

Neonatal vaccination of mice with bacteria prevents cockroach-induced asthma as adults – News Medical

Bacteria and bugs in guts and gallbladders – Claire O’Connell – The Irish Times

October 24, 2016

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Strain-level associations of gut microbes, symbiosis in a coral reef sponge, halophilic microbiota of table salt, and microbiota of the red snapper.

Pregnancy and early life

Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling – Francesco Asnicar – bioRxiv Preprint

Human oral microbiome

Salivary microbiota and caries occurrence in Mutans Streptococci-positive school children – M. ElSalhy – European Journal of Paediatric Dentistry

Microbiological and bioinformatics analysis of primary Sjögren’s syndrome patients with normal salivation – Huma Siddiqui – Journal of Oral Microbiology

Evaluation of buccal cell samples for studies of oral microbiota – Guoqin Yu – Cancer Epidemiology, Biomarkers & Prevention

Human gut microbiome

Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns – Francesca De Filippis – Microbiome

Review: The role of the commensal microbiota in adaptive and maladaptive stressor-induced immunomodulation – Amy R. Mackos – Hormones and Behavior

Review: Health Disparities and the Microbiome – Keisha Findley – Trends in Microbiology

Review: Emerging Technologies for Gut Microbiome Research – Jason W. Arnold – Trends in Microbiology

Review: Tiny microbes, enormous impacts: what matters in gut microbiome studies? – Justine Debelius – Genome Biology

Animal models

Illumina Miseq platform analysis caecum bacterial communities of rex rabbits fed with different antibiotics – Fuqin Zou – AMB Express

Animal microbiome

Draft Genomes Shed Light on the Dual Bacterial Symbiosis that Dominates the Microbiome of the Coral Reef Sponge Amphimedon queenslandica – Marie-Emilie A. Gauthier – Frontiers in Marine Science

Plant, root, and soil microbiome

Assessing the role of endophytic bacteria in the halophyte Arthrocnemum macrostachyum salt tolerance – S. Navarro-Torre – Plant Biology

Control of Cortaderia selloana with a glyphosate-based herbicide led to a short-term stimulation of soil fungal communities – M. Anza – Environmental Monitoring and Assessment

Water and extremophile microbiome

Trade-off between taxon diversity and functional diversity in European lake ecosystems
– Lars Grossmann – Molecular Ecology

Diversity of retrievable heterotrophic bacteria in Kongsfjorden, an Arctic fjord –
Rupesh Kumar Sinha – Brazilian Journal of Microbiology

Atmospheric aerosol deposition influences marine microbial communities in oligotrophic surface waters of the western Pacific Ocean – Teruya Maki – Deep Sea Research Part I: Oceanographic Research Papers

Long-term dynamics in microbial eukaryotes communities: a paleolimnological view based on sedimentary DNA – Eric Capo – Molecular Ecology

Shifts in bacterial community structure during succession in a glacier foreland of the High Arctic – Mincheol Kim – FEMS Microbiology Ecology

Food microbiology

Microbial culturomics unravels the halophilic microbiota repertoire of table salt: Description of Gracilibacillus massiliensis sp. nov. – Awa Diop – Microbial Ecology in Health and Disease

Microbiota of wild-caught Red Snapper Lutjanus campechanus – Andrea M. Tarnecki – BMC Microbiology

Archaea

Archaea in Natural and Impacted Brazilian Environments – Thiago Rodrigues – Archaea

Fungi

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

Metagenomics and bioinformatics

Filtration and Normalization of Sequencing Read Data in Whole-Metagenome Shotgun Samples – Philippe Chouvarine – PLOS ONE

Review: Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes – Boahemaa Adu-Oppong – Annals of the New York Academy of Sciences

Review: Translational metagenomics and the human resistome: confronting the menace of the new millennium – Matthias Willmann – Journal of Molecular Medicine

Metabolomics

Review: The Human Microbiome and Metabolomics: Current Concepts and Applications – Eric Banan-Mwine Daliri – Critical Reviews in Food Science and Nutrition

Microbes in the news

Post publication peer review of mSystems migraine paper – Jonathan Eisen – Storify

Woods Hole Oceanographic Institution Teams Up on Coral Study – Cape Cod

Costly detox programmes slammed by nutrition experts – Susan Strongman – NZ Herald

The Nose Knows Beneficial Bacteria – Lindsey Bomar – ASM blog

Ph.D. student creates new way to treat antibiotic resistance – CCTV America

‘My father’s poo saved my life’: Woman who could not leave her bed due to her agonising chronic constipation reveals how a VERY personal transplant saved her life – Sophie Haslett – Daily Mail

 

October 21, 2016

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Oral bacteria in esophageal cancer samples, spring blooms of coastal phytoplankter, and a microbial anthropologist in the Jungle.

Events

Meeting: Chemistry of Microbiomes in Human Environments – 11/9/16 – Jonathan Eisen – MicroBEnet

Human oral microbiome

Human Microbiome Fusobacterium Nucleatum in Esophageal Cancer Tissue Is Associated with Prognosis – Kensuke Yamamura – Clinical Cancer Research

Press: Presence of certain oral bacterium in esophageal cancer samples associated with shorter survival – Medical Xpress

Human vaginal microbiome

Review: Role of microbial flora in female genital tract: A comprehensive review – Subramanyam Dasari – Asian Pacific Journal of Tropical Disease

Plant, root, and soil microbiome

Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L.) Peeling – Jiachao Zhang – PLOS ONE

Diversity indices using arbuscular mycorrhizal fungi to evaluate the soil state in banana crops in Colombia – Germán Mahecha-Vásquez – Applied Soil Ecology

Water microbiome

Physiological and ecological drivers of early spring blooms of a coastal phytoplankter – Kristen R. Hunter-Cevera – Science

Microbial community dynamics in semi-commercial RAS for production of Atlantic salmon post-smolts at different salinities – Ingrid Bakke – Aquacultural Engineering

Deep-sequencing of the bacterial microbiota in commercial-scale recirculating and semi-closed aquaculture systems for Atlantic salmon post-smolt production – Ida Rud – Aquacultural Engineering

Built environment microbiome

Shoe soles as a potential vector for pathogen transmission: a systematic review – T. Rashid – Journal of Applied Microbiology

Microbes in the news

A Microbial Anthropologist in the Jungle – Maria Gloria Dominguez-Bello – Cell

African Soil Microbiology Project – Elizabeth Bach – Global Soil Biodiversity

Researchers Say Plant Bacteria Could Provide its Own Salvation – Interesting Engineering

I’m a Doctor. If I Drop Food on the Kitchen Floor, I Still Eat It. – Aaron E. Carroll – The New York Times
Letters to the Editor: Eat Food From the Floor? Microbiology and Mores – The New York Times

Dr Brad McKay explains the complex world of vaginal bacteria – Brad McKay – News.com.au

What’s making lifeguards sick at La Jolla Cove? – Brandon Lewis – CBS8

Spotlight on Grants: Nickel and cobalt in Streptococcus – Siti Nur Amalina – Microbe Post

ASM’s Microbes After Hours Microbes After Hours: The Necrobiome – Microbial Life After Death

Bik’s Non-Microbiology Picks

We used to sell cigarettes in hospitals. 5 practices that may soon look just as outdated – Melissa Bailey – STAT News

October 20, 2016

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Events

2016-2017 Dannon Gut Microbiome, Yogurt and Probiotics Fellowship Grant Application Form
Also see: Leading Yogurt Company Challenges Students to Unearth New Data on the Gut Microbiome, Yogurt and Probiotics with $50K Grant Program. Dannon® will award two $25K grants to further scientific research – PR Newswire

Third Annual Microbiome Symposium – Penn Vet – October 26 and 27, 2016
Penn’s microbiome conference turns eye toward antibiotic use in livestock
Text by Katherine Unger Baillie – Penn Current

Q4 microbiome conferences roundup: Are you looking for a good scientific microbiome research symposium? Over the next three months, you have six exciting microbiome conferences from which to choose. – Megan M. MacBride – Taconic

Disappointing lack of diversity here: #YAMMM: 29 speakers, 4 women. Microbiome Drug Development Summit, 24-26 January 2017, Paris, France

General microbiome

An introduction to microbiome analysis for human biology applications – Katherine R. Amato – American Journal of Human Biology

Human oral microbiome

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Human respiratory microbiome

Role of microbiome in the pathophysiology and disease course of asthma – Singanayagam A – Curr Opin Pulm Med

Human skin microbiome

Review: Topographical and physiological differences of the skin mycobiome in health and disease – Jay-Hyun Jo – Virulence

Human vaginal microbiome

A fruitful alliance: the synergy between Atopobium vaginae and Gardnerella vaginalis in bacterial vaginosis-associated biofilm – Liselotte Hardy – Sexually Transmitted Infections

Human gut microbiome

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Similar Fecal Microbiota Signatures in Patients With Diarrhea-Predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

Review: Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches – R. Balfour Sartor – Gastroenterology

Review: The Microbiome and Human Disease Pathogenesis: How do you do what you do to me …? – Edward N. Janoff – Translational Research

Animal models

Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing – Geon Goo Hana – Veterinary Microbiology

Alterations of the Host Microbiome Affect Behavioral Responses to Cocaine – Drew D. Kiraly – Scientific Reports

Animal microbiome

Developmental and ecological benefits of the maternally transmitted microbiota in a dung beetle – Daniel B. Schwab – The American Naturalist

Microbiome analysis shows enrichment for specific bacteria in separate anatomical regions of the deep-sea carnivorous sponge Chondrocladia grandis – Joost T.P. Verhoeven – FEMS Microbiology Ecology Letters

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities – Jessica L. Ray – Molecular Ecology

Spatial Microbial Composition Along the Gastrointestinal Tract of Captive Attwater’s Prairie Chicken – Yan Zhang – Microbial Ecology

Plant, root, and soil microbiome

Nestedness in Arbuscular Mycorrhizal Fungal Communities along Soil pH Gradients in Early Primary Succession: Acid-Tolerant Fungi Are pH Generalists – Ai Kawahara – PLOS ONE

Review: Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture – Yuan Qin – Biotechnology Advances

Water microbiome

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor – Katsunori Yanagawa – ISME J

More microbiology

Correspondence: Improving Microbiology Research: the Problems Are Less Statistical and More Biological – Dennis F. Lawler – mBio

What’s in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015 – Erik Munson – Journal of Clinical Microbiology

Microbes in the news

Tasmanian devil milk fights superbugs – BBC News
Tasmanian devil milk kills several deadly superbugs that are resistant to existing drugs – Science Alert

There’s a breast microbiome, and it’s different in women with breast cancer – Erin Blakemore – Washington Post

Research Highlight: A protective protozoan in mucosal infection – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Outbreak of Biofilm-Forming Achromobacter xylosoxidans Due to Environmental Transmission – Infection Control Today

The Emergent Microbiome: A Revolution for the Life Sciences – Part VII, The Microbiome and Immunotherapy I – Dilworth IP – Lexology

New science museum exhibit explores ‘the secret world’ inside us: N.C. Museum of Natural Sciences in downtown Raleigh opens a new special exhibit this weekend – WRAL.com

Vedanta Biosciences Granted First European Patent Broadly Covering Pharmaceutical Compositions for Microbiome Therapeutics Based on Bacterial Consortia – Business Wire

Science, publishing, and career

Married to the(ir) job: living with an academic. Scholars and their significant others share the good, the bad and the ugly – Times Higher Education

Investigation Finds Pathologist Guilty of Systemic Misconduct – Bob Grant – The Scientist

Women need to be seen and heard at conferences. A neuroscience initiative is boosting the number of female invited speakers at meetings. Other disciplines should do the same – Nature

The Bearded Lady Project . Q&A: Lexi Jamieson Marsh and Ellen Currano: Face to face – Alexandra Witze – Nature

October 19, 2016

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Blogging from SJC today on my way to Vancouver. Oral microbes correlated with food-triggered migraines, spinal cord injuries, comparison of 8 DNA extraction kits on 3 sample types, mockrobiota.

Jobs and Events

Flying to Vancouver today to give a short talk at DNA Genotek’s Microbiome Breakfast Session at #ASHG2016

Fall Mid-Atlantic Microbiome Meetup (M3) – November 1-2, University of Maryland

Human oral microbiome

Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort – Antonio Gonzalez – mSystems

Press: Migraines could be caused by gut bacteria, study suggests – Hannah Devlin – The Guardian
Scientists think they’ve found why chocolates and wine cause migraines for some very unlucky people – Katherine Ellen Foley – Quartz

Human skin microbiome

The skin is a significant but overlooked anatomical reservoir for vector-borne African trypanosomes – Paul Capewell – eLife

Human respiratory microbiome
The Prevalence of Antibiotic-resistant Staphylococcus aureus Nasal Carriage among Industrial Hog Operation Workers, Community Residents, and Children Living in their Households: North Carolina, USA – Sarah M. Hatcher – Environmental Health Perspectives

Press: Drug-resistant staph bacteria prevalence higher in young children living with hog workers – EurekAlert

Animal models

Gut dysbiosis impairs recovery after spinal cord injury – Kristina A. Kigerl – Journal of Experimental Medicine

Press: Researchers show how spinal cord injury causes profound changes in gut microbiota – News-Medical Net
Gut bacteria can aid recovery from spinal cord injury, study suggests – Science Daily

Techniques

Eight commercial kits, 16 procedures, 3 sample types: Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition – Berith E. Knudsen – mSystems

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking – Nicholas A. Bokulich – mSystems

Bioinformatics and metagenomics

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography – Stephen Nayfach – Genome Research

Press: From Genome Research: Strain-level profiling yields new insights into mother-infant microbiomes – EurekAlert

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data – Sandeep J. Joseph – PeerJ

Microbes in the news

Tapping the Human Gut Microbiome, Part 1: The Next Frontier for Novel Therapeutics – Christian Furlan Freguia – GenEngNews
Tapping the Human Gut Microbiome, Part 2: From the Bottom Up – Christian Furlan Freguia – GenEngNews

The microbiome: Looking at microbes as more than pathogens – Ryan T. Ranallo – Healio

Harnessing The Plant Microbiome For Cleaner, Pesticide-Free Agriculture – Ben Schiller – FastCoexist

Bacteria named in Mighty Taco outbreak; chain denies fault – Food Safety News

Clemson students get bacteria named after them. New strain of Legionella named for students who studied it – Carla Field – Wyff4

Bacteria ‘alarm clock’ may cause repeat infections in patients – Kate Wighton – Imperial.ac.uk

Microbes and Money

Igniting a Microbiome Revolution: Era7 Bioinformatics Syncs with Capital Cell – Erin Hobey – CrowdFundInsider
Igenbio Inc offers metagenome analysis services for clinical and industrial applications – Reuters

October 18, 2016

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Vaginal probiotics, forensic analysis of skin bacteria on fabrics, Wolbachia in nematodes, ivy phyllosphere, microbial life in two polar extremes, how to improve the indoor environment, and mass spec analysis of human habitat molecules.

Pregnancy and early life

Vaginal Probiotic Administration in the Management of Preterm Premature Rupture of Membranes – Daskalakis G.J. – Fetal Diagnosis and Therapy

General human microbiome

Review: Health Disparities and the Microbiome – Keisha Findley – Trends in Microbiology

Human respiratory microbiome

Review: Host–Bacterial Crosstalk Determines Staphylococcus aureus Nasal Colonization – Michelle E. Mulcahy – Trends in Microbiology

Human skin and tissue microbiome

Forensic analysis using microbial community between skin bacteria and fabrics – So-Yeon Lee – Toxicology and Environmental Health Sciences

Not a word about extraction controls, so proceed with caution: Bacterial Communities Associated with Atherosclerotic Plaques from Russian Individuals with Atherosclerosis – Elvira E. Ziganshina – PLOS ONE

Human gut microbiome

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients – Lianshuo Li – Genomics, Proteomics & Bioinformatics

Review: Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

Review: The gut microbiota and gastrointestinal surgery – Kristina Guyton – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiota and Risk of Developing Celiac Disease – Cenit, Maria C. – Journal of Clinical Gastroenterology

Editorial: What’s in Your GI Microbiome? – Martin H. Floch – Journal of Clinical Gastroenterology

Animal and in vitro models

Study of the Ability of Bifidobacteria of Human Origin to Prevent and Treat Rotavirus Infection Using Colonic Cell and Mouse Models – Mélanie Gagnon – PLOS ONE

Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism – Limin Zhang – mSystems

A mixture of milk and vegetable lipids in infant formula changes gut digestion, mucosal immunity and microbiota composition in neonatal piglets – Isabelle Le Huërou-Luron – European Journal of Nutrition

An Advanced In Vitro Technology Platform to Study the Mechanism of Action of Prebiotics and Probiotics in the Gastrointestinal Tract – Marzorati, Massimo – Journal of Clinical Gastroenterology

Animal microbiome

Sea lions: Protein and RNA extraction from mucosal swabs: a minimally invasive source of ecological data for studies of natural populations – W Espinosa-de Aquino – Methods in Ecology and Evolution

Mycobacteria in aquarium fish: results of a 3-year survey indicate caution required in handling pet-shop fish – D Kušar – Journal of Fish Diseases

Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts – Amanda M. V. Brown – Scientific Reports

Plant, root, and soil microbiome

Disentangling interactions between microbial communities and roots in deep subsoil – Martina I. Gocke – Science of the Total Environment

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock – Alexandre Bagnoud – Nature Communications

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area – Isabella Gandolfi – Environmental Pollution

Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation – Xihui Xu – Environmental Science and Pollution Research

Impact of urban land use on the bacterial phyllosphere of ivy (Hedera sp.) – Wenke Smets – Atmospheric Environment

Water and extremophile microbiome

Periodic change in coastal microbial community structure associated with submarine groundwater discharge and tidal fluctuation – Eunhee Lee – Limnology and Oceanography

Microbial Community Dynamics in Two Polar Extremes: The Lakes of the McMurdo Dry Valleys and the West Antarctic Peninsula Marine Ecosystem – Jeff S. Bowman – BioScience

Diversity and physiological and biochemical properties of heterotrophic bacteria isolated from Lake Baikal neuston – A. D. Galach’yants – Microbiology

Phylogenetic and functional prokaryotic diversity in the Hoito-Gol mesothermal mineral spring (Eastern Sayan Mountains, Buryat Republic) – E.S. Kashkak – Microbiology

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water – Xiao-Ming Lu – Microbial Ecology

Built environment microbiome

How do we make indoor environments and healthcare settings healthier? – Jack A. Gilbert – Microbial Biotechnology

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats – Daniel Petras – Analytical Chemistry

Food microbiology

Raw Ready-to-Eat Seafood Safety: Microbiological Quality of the Various Seafood Species Available at Fishery, Hyper, and Online Market – H.W. Kim – Letters in Applied Microbiology

Bioinformatics and metagenomics

MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources – Nicolas Tsesmetzis – Standards in Genomic Sciences

IMG/M: integrated genome and metagenome comparative data analysis system
I-Min A. Chen – Nucleic Acids Research

Review: The present and future of de novo whole-genome assembly – Jang-il Sohn – Briefings in Bioinformatics

Microbes in the news

Soaking A Bunch Of Toads In Their Own Bacteria Could Save Their Lives – Krista Langlois – Five Thirty Eight

Bacteria Hysteria

Why your office could be making you sick: Keyboards ‘contain 20,000 MORE bacteria than a toilet bowl’– Stephen Matthews – Daily Mail

How to clean and disinfect your keyboard and mouse – Ed Rhee – CNET

Science, publishing, and career

A Tale of Two Women and Their Careers in Science – Anna Katie – YouTube

Promoting Responsible Scientific Research – American Society for Microbiology

October 17, 2016

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Fecal markers on child hands in Bangladesh, Clostridium difficile in pet dogs, intertidal microbes, and variability in household airborne bacteria.

Human skin microbiome

Occurrence of host-associated fecal markers on child hands, household soil, and drinking water in rural Bangladeshi households – Alexandria B. Boehm – Environmental Science & Technology Letters

Human respiratory microbiome

Data Mining of Lung Microbiota in Cystic Fibrosis Patients – Jianguo Li – PLOS ONE

Review: A future perspective on neurodegenerative diseases: Nasopharyngeal and gut microbiota – Fazlurrahman Khan – Journal of Applied Microbiology

Human urinary and reproductive tract

Methods only, no results (or: how to write two papers instead of one): Methodology for a vaginal and urinary microbiome study in women with mixed urinary incontinence – Yuko M. Komesu – International Urogynecology Journal

Human oral microbiome

Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study – Xiaozhou Fan – Gut

Human gut microbiome

High-throughput sequencing identifies distinct fecal and mucosal gut microbiota correlating with different mucosal proteins – Li-na Dong – PeerJ Preprint

Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder – Ping Lin – Journal of Affective Disorders

Differential Changes in Gut Microbiota After Gastric Bypass and Sleeve Gastrectomy Bariatric Surgery Vary According to Diabetes Remission – Rinki Murphy – Obesity Surgery

Review: Antibiotics and the Intestinal Microbiome : Individual Responses, Resilience of the Ecosystem, and the Susceptibility to Infections – Sophie Thiemann – Current Topics in Microbiology and Immunology

Animal experiments

Chronic Sleep Disruption Alters Gut Microbiota, Induces Systemic and Adipose Tissue Inflammation and Insulin Resistance in Mice – Valeriy A. Poroyko – Scientific Reports

The impact of orally administered phages on host immune response and surrounding microbial communities – Yingying Hong – Bacteriophage

Animal microbiome

More than 50% of Clostridium difficile Isolates from Pet Dogs in Flagstaff, USA, Carry Toxigenic Genotypes – Nathan E. Stone – PLOS ONE

Press: NAU Crew Finds Bacteria Clue by Scooping Pooch Poo – Arizona Public Media

Rumen microbiota for wild boreal cervids living in the same habitat – Kjartan Østbye – FEMS Microbiology Letters

Structure and culture of the gut microbiome of the Mormon cricket Anabrus simplex – Chad C Smith – bioRxiv Preprint

Plant, root, and soil microbiome

Microbial legacies alter decomposition in response to simulated global change – Jennifer BH Martiny – ISME Journal
Water microbiome

Spatial and Halophytes Associated Microbial Communities in Intertidal Coastal Region of India – Doongar R. Chaudhary – International Journal of Phytoremediation

Built environment microbiome

High temporal variability in airborne bacterial diversity and abundance inside single-family residences – Joanne B. Emerson – Indoor Air

Microbes in the news

UMass microbiologist Kristen DeAngelis awarded $2.5 million grants to study how soil microbes contribute to global warming – Lucas Ropek

Bdellovibrio, the cannibalistic drug coming to humanity’s rescue – Mallory Locklear – Ars Technica

Nuclear Waste Repositories Safer With Bacteria – iTechPost

UA Museum hopes to display giant whale skeleton after bacteria clean up the bones for a couple of years – Dermot Cole – ADN

Nikon Small World Photomicrography Competition Popular Vote Gallery

October 14, 2016

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The pubic hair microbiome, lung transplant virome, IBS microbiome signature, coprolites, antibacterial molecules for babies the Tasmanian Devil pouch, Archaea in Mars simulation, white pudding, functional mapping pipeline,

Human oral microbiome

Clinical, Immune, and Microbiome Traits of Gingivitis and Peri-implant Mucositis – G.P. Schincaglia – Journal of Dental Research

The microbial community shifts of subgingival plaque in patients with generalized aggressive periodontitis following non-surgical periodontal therapy: a pilot study – Jing Hang – Oncotarget

Review: The Autoimmunity-Oral Microbiome Connection – N Nikitakis – Oral Diseases

Human respiratory microbiome

The Perioperative Lung Transplant Virome: Torque Teno Viruses are Elevated in Donor Lungs and Show Divergent Dynamics In Primary Graft Dysfunction – A. A. Abbas – American Journal of Transplantation

Composition and immunological significance of the upper respiratory tract microbiota – L. Patrick Schenck – FEBS Letters

Human skin and hair microbiome

Individualization of pubic hair bacterial communities and the effects of storage time and temperature – Diana W. Williams – Forensic Science International: Genetics

Gram-positive anaerobe cocci (GPAC) are underrepresented in the microbiome of filaggrin-deficient human skin – Patrick L.J.M. Zeeuwen – The Journal of Allergy and Clinical Immunology

Review: Microbiome in healthy skin, update for dermatologists – B. Dréno – Journal of the European Academy of Dermatology and Venereology

Human reproductive tract microbiome

Challenging dogma: the endometrium has a microbiome with functional consequences! – Linda C. Giudice – American Journal of Obstetics & Gynecology

Human gut microbiome

Intestinal microbiota in adult patients with Short Bowel Syndrome: Preliminary results from a pilot study – Stefania Boccia – Clinical Nutrition

Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome – Julien Tap – Gastroenterology

The dual role of Escherichia coli in the course of ulcerative colitis – Magdalena Pilarczyk-Zurek – BMC Gastroenterology

Review: The gut microbiota and gastrointestinal surgery – Kristina Guyton – Nature Reviews Gastroenterology & Hepatology

Review: Dysbiosis in the ICU: Microbiome science coming to the bedside – Georgios D Kitsios – Journal of Critical Care

Review: Parasites, microbiota and metabolic disease – Sonakshi Bhattacharjee – Parasite Immunology

Review: Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

Review: Human Coprolites as a Source for Paleomicrobiology – Sandra Appelt – Microbiology Spectrum

Animal models

Behavioural and Neurochemical Consequences of Chronic Gut Microbiota Depletion during Adulthood in the Rat – A.E. Hoban – Neuroscience

Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses – Zhipeng Li – Environmental Microbiology Reports

Microbial community mapping in intestinal tract of broiler chicken – Yingping Xiao – Poultry Science

Animal microbiome

Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria – Jeroen A. J. M. van de Water – Microbial Ecology

Cathelicidins in the Tasmanian devil (Sarcophilus harrisii) – E. Peel – Scientific Reports

Plant, root, and soil microbiome

Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems – S. Uroz – Soil Biology and Biochemistry

Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea – Ludovic Henneron – Oikos

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat – Akitomo Kawasaki – PLOS ONE

Review: Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions – Vishal Kumar – Frontiers in Plant Science

Water microbiome

Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes – M. Romina Schiaffino – Environmental Microbiology

Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams – Peter S. Levi – Oikos

Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake – Patricia M. Valdespino-Castillo – Microbial Ecology

Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River – Wenhui Wang – Scientific Reports

Microbes in space

Survivability and Growth Kinetics of Methanogenic Archaea at various pHs and Pressures: Implications for Deep Subsurface Life on Mars – Navita Sinha – Planetary and Space Science

Food microbiology

The use of 16S rRNA gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: The example of white pudding – Emilie Cauchie – International Journal of Food Microbiology

Microbial diversity in pitted sweet cherries (Prunus avium L.) as affected by high-hydrostatic pressure treatment – Julia Toledo del Árbol – Food Research International

Built environment microbiology

Bioaerosol assessment in the library of Istanbul University and fungal flora associated with paper deterioration – Duygu Göksay Kadaifciler – Aerobiologia

Techniques / Fungi

Accurate Estimation of Fungal Diversity and Abundance Through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing – D. Lee Taylor – Applied and Environmental Microbiology

Bioinformatics and metagenomics

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli – Minseung Kim – Nature Communications

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies – Jiwoong Kim – BMC Bioinformatics

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets – Rico Lucas – FEMS Microbiology Ecology

Microbes in the news

Extremophiles found in a lake, and this is great news for biotech – Colm Gorey – Silicon Republic

‘I want my teeth back’: Kids infected with jaw-eating bacteria after dental treatment – Katie Mettler – Sacramento Bee

Microbiome biotech joins Peter Thiel’s Breakout Labs project – Fierce Biotech

Science, publishing, and career

Book:  Fungible Life: Experiment in the Asian City of Life – Aihwa Ong – Amazon

October 12, 2016

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Infants with bronchiolitis, vitamin D receptor GWAS study, long-term effects of stool transplants, genome reduction in insect endosymbionts, San Francisco Bay denitrifying communities, resistomes in metagenomic datasets, Picodroplet WGA for metagenomics.

Jobs and events

Scientist/Senior Scientist opening at WholeBiome

Upcoming mothur and R workshops – Pat Schloss – Mothur

Pregnancy and early life

Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk – Manli Y. Davis – Microbiome

Human general and multisite microbiome

Multi-Body-Site Microbiome and Culture Profiling of Military Trainees Suffering from Skin and Soft Tissue Infections at Fort Benning, Georgia – Jatinder Singh – mSphere

Review: The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review – Rosario Lucas López – APMIS

Human oral microbiome

Does obesity influence the subgingival microbiota composition in periodontal health and disease? – Suellen da Silva Maciel – Journal of Clinical Periodontology

Human respiratory microbiome

Throat Swabs and Sputum Culture as Predictors of P. aeruginosa or S. aureus Lung Colonization in Adult Cystic Fibrosis Patients – Darius Seidler – PLOS ONE

Association of nasopharyngeal microbiota profiles with bronchiolitis severity in infants hospitalised for bronchiolitis – Kohei Hasegawa – European Respiratory Journal

Human urinary tract microbiome

Changes in Urinary Microbiome Populations Correlate in Kidney Transplants With Interstitial Fibrosis and Tubular Atrophy Documented in Early Surveillance Biopsies –
B. D. Modena – American Journal of Transplantation

Human reproductive tract microbiome

Evidence that the endometrial microbiota has an effect on implantation success or failure – Immaculada Moreno – American Journal of Obstetrics & Gynecology

Human gut microbiome

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes – Anna Heintz-Buschart – Nature Microbiology

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota – Jun Wang – Nature Genetics

A Pair of Identical Twins Discordant for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Differ in Physiological Parameters and Gut Microbiome Composition – Ludovic Giloteaux – American Journal of Case Reports

Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis – Wenjun Liu – Scientific Reports

Long-term effects on luminal and mucosal microbiota and commonly acquired taxa in faecal microbiota transplantation for recurrent Clostridium difficile infection – Jonna Jalanka – BMC Medicine

Press: Healing effect of fecal microbiota transplantation lasts for long – Science Daily

Integrity of the Human Faecal Microbiota following Long-Term Sample Storage – Elahe Kia – PLOS ONE

Review: Signals from the gut microbiota to distant organs in physiology and disease -Bjoern O Schroeder – Nature Medicine

Review: The Gut Microbiome as Therapeutic Target in Central Nervous System Diseases: Implications for Stroke – Katarzyna Winek – Neurotherapeutics

Review: The Multibiome: The Intestinal Ecosystem’s Influence on Immune Homeostasis, Health, and Disease – Heather A Filyk – EBioMedicine

Commentary: Microbiome: Should we diversify from diversity? – Katerina V.-A. Johnson – Gut Microbes

Review: I-Cubed (Infection, Immunity, and Inflammation) and the Human Microbiome – David S. Younger – Neurologic Clinics

Animal models

Microbiota of the Small Intestine Is Selectively Engulfed by Phagocytes of the Lamina Propria and Peyer’s Patches – Masatoshi Morikawa – PLOS ONE

Spatial and Temporal Shifts in Bacterial Biogeography and Gland Occupation during the Development of a Chronic Infection – Daniela Keilberg – mBio

Altered gut microbiota in female mice with persistent low body weights following removal of post-weaning chronic dietary restriction – Jun Chen – Genome Medicine

Animal microbiome

Mosquitoes host communities of bacteria that are essential for development but vary greatly between local habitats – Kerri L. Coon – Molecular Ecology

Review: Dissecting genome reduction and trait loss in insect endosymbionts – Amparo Latorre – Annals of the New York Academy of Sciences

Review: Beneficial microorganisms for honey bees: problems and progresses – Daniele Alberoni – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

The interplay between soil structure, roots, and microbiota as a determinant of plant–soil feedback – Joana Bergmann – Ecology and Evolution

Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees – O. Nicolitch – Soil Biology and Biochemistry

Bacterial selection for biological control of plant disease: criterion determination and validation – Monalize Salete Mota – Brazilian Journal of Microbiology

Killing two birds with one stone: Natural rice rhizospheric microbes reduce arsenic uptake and blast infections in rice – Venkatachalam Laksmanan – Frontiers in Plant Science

Bioenergy cropping systems that incorporate native grasses stimulate growth of plant-associated soil microbes in the absence of nitrogen fertilization – Lawrence G. Oates – Agriculture, Ecosystems & Environment

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat – Akitomo Kawasaki – PLOS ONE

Review: Chatting With a Tiny Belowground Member of the Holobiome: Communication Between Plants and Growth-Promoting Rhizobacteria – R. Sharifi – Advances in Botanical Research

Water and extremophile microbiome

Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance – Jessica A. Lee – Microbial Ecology

Molecular diversity of plankton in a tropical crater lake switching from hyposaline to subsaline conditions: Lake Oloidien, Kenya – Wei Luo – Hydrobiologia

Distinct biogeographical patterns of marine bacterial taxonomy and functional genes – John Matthew Haggerty – Global Ecology and Biogeography

Waste and pollution microbiology

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system – Jiaojiao Niu – Scientific Reports

Comparison of the microbial community composition of pristine rock cores and technical influenced well fluids from the Ketzin pilot site for CO2 storage – Linda Pellizzari – Environmental Earth Sciences

Food microbiology

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir – Aaron M. Walsh – mSystems

Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase – Ahmed Abdelfattah – Horticulture Research

Bioinformatics and metagenomics

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis – Maria Hammond – Microbiome

The structure and diversity of human, animal and environmental resistomes – Chandan Pal – Microbiome

 

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees – Wen Huang – Molecular Biology and Evolution

 

Proteomics

Mining gut microbiome oligopeptides by functional metaproteome display – Jonas Zantow – Scientific Reports

More microbiology

Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron – Nathan D. Schwalm III – mBio

Living together in biofilms: the microbial cell factory and its biotechnological implications – Mercedes Berlanga – Microbial Cell Factories

Microbes in the news

The Virus With Spider DNA. How did part of a black-widow venom gene end up in a virus that infects one of the world’s most successful bacteria? – Ed Yong – The Atlantic

The Human Microbiome – ASM Cultures microbiome special featuring top scientists and biotech companies

The superhero in your vagina – Kendall Powell – Mosaic Science

Legionella Bacteria Detected at 4 American Airlines Hangars – ABC News

Study Sees Link Between Allergies and the Infant Gut – Robert Lee Hotz – Wall Street Journal

Breasts have their own microbiome – and it could influence your cancer risk
Your breast has its own unique ecosystem – Bec Crew – Science Alert

Researchers restored a colony of microbes in the gut – Ian Graber-Stiehl – Popular Science

Microbes and money

Second Genome Partners with King’s College London to Evaluate the Influence of the Microbiome in Landmark EAT Study – PR Newswire

MicroBiome Therapeutics’ NM504 For Improving Blood Glucose Regulation Is First Microbiome Modulator to Receive U.S. Patent Allowance – PR Web

Seres’s pioneering microbiome drug fails mid-stage trial – Mark Ratner

Farmers Are Manipulating Microbiomes to Help Crops Grow – Sarah Zhang – Wired