Category Archives: Events and jobs

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

 

Storify San Francisco Microbiome Meetup #SFBiome

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It’s been a long day, but here is a Storify on the SF Microbiome Meetup at IndieBio, a biotech startup accelerator in San Francisco. Thanks, George Roche, Stephen Martis, and host Jun Axup for organizing! We had a bigger audience than we anticipated, but we could not say no to anyone who showed up.

My apologies for some typos…. I am better at Twitter when I got a bigger keyboard!

Storify on the SF Microbiome Meetup at IndieBio

Cover photo by Alexander Probst, @AlexJProbst

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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 26, 2016

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Discount on San Diego Microbiome Congress, sleep deprivation, constipation, strange structures in blood are not bacteria, complexity in corals, grape microbiota, microbial corrosion.

Events

North American Microbiome Congress – San Diego, 24-25 January 2017. This is the conference that was criticized online by Jonathan Eisen (see here) and me about the initial lack of diversity in the speaker line-up. The organizers have taken this to heart, apologized, and will make an effort to do better in the future. After talking to the organizers, they are offering my readers a 15% discount code ‘DIGEST15’ on the conference fee. There are also reduced priced Early Bird tickets available until 31st October 2016.

Human respiratory microbiome

Re-emergence of Lower Airway Microbiota in Cystic Fibrosis Lung Transplant Patients – Saad A Syed – Annals of the American Thoracic Society

Human gut microbiome

Gut Microbiota and Glucometabolic Alterations in Response to Recurrent Partial Sleep Deprivation in Normal-weight Young Individuals – Christian Benedict – Molecular Metabolism

Press: Sleep loss tied to changes of the gut microbiota in humans – Science Daily
Sleep loss may be linked to changes in gut bacteria levels – Ryan Maass – UPI

Characterization of Microbiota in Children with Chronic Functional Constipation – Tim G. J. de Meij – PLOS ONE

Microbiome of nearly-sterile sites

Pleomorphic Structures in Human Blood Are Red Blood Cell-Derived Microparticles, Not Bacteria – Adam J. Mitchell – PLOS ONE

Animal models

Antibiotic effects on gut microbiota and metabolism are host dependent – Shiho Fujisaka – The Journal of Clinical Investigation

Diversity and resilience of the wood-feeding higher termite Mironasutitermes shangchengensis gut microbiota in response to temporal and diet variations – Ying Wang – Ecology and Evolution

Animal microbiome

Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes – Amy Apprill – mSystems

Plant, root, and soil microbiome

Looking for Rhizobacterial Ecological Indicators in Agricultural Soils Using 16S rRNA metagenomic Amplicon Data – José R. Valverde – PLOS ONE

Biochar-stimulated plant performance is strongly linked to microbial diversity and metabolic potential in the rhizosphere – Max Kolton – New Phytologist

Wine microbiology is driven by vineyard and winery anthropogenic factors – Cédric Grangeteau – Microbial Biotechnology

Effect of 40 and 80 Years of Conifer Regrowth on Soil Microbial Activities and Community Structure in Subtropical Low Mountain Forests – Ed-Haun Chang – Forests

Water microbiome

mdRNA-Seq analysis of marine microbial communities from the northern Red Sea – Shengwei Hou – Scientific Reports

Assessing Marine Microbial Induced Corrosion at Santa Catalina Island, California – Gustavo A. Ramírez – Frontiers in Microbiology

Bioreactor microbiology

Wow, this paper will cost you $63: Diversity of Microbial Communities in Biogas Reactors – Bernadett Pap – Current Biochemical Engineering

Viruses and phages

Viral Metagenomics on Blood-Feeding Arthropods as a Tool for Human Disease Surveillance – Annika Brinkmann – Int J Mol Sci

Techniques

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

Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices – David A. Selck – PLOS ONE

Microbes in the news

Reef rehab could help threatened corals make a comeback. Solutions for threatened reefs vary by location and damage done – Amy McDermott – Science News

Bacteria get dangerously weird in space – Shayla Love – Washington Post

Cranberry extract disrupts communication between bacteria linked to pervasive infections – News Medical Net

LSU alumna Kaitlynn Fenley teaches microbiology cooking class – Allie Cobb – The Daily Reveille

NIH research project will upgrade ‘metagenomics’ system – Purdue

Science, publishing, and career

Beyond Traditional Scientific Training: The Importance of Community and Empowerment for Women in Ecology and Evolutionary Biology – M. Claire Horner-Devine – Frontiers in Ecology and Evolution

October 25, 2016

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Bat skin microbiome, carnivorous sponges, metagenome of an aquifer, and nitrogen fixation in symbionts of marine invertebrate animals.

Human respiratory microbiome

Microbial communities of conducting and respiratory zones of lung-transplanted patients – Marie Beaume – Frontiers in Microbiology

Animal microbiome

Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment – Christine V. Avena – Frontiers in Microbiology

The Microbiome and Occurrence of Methanotrophy in Carnivorous Sponges – Jon T. Hestetun – Frontiers in Microbiology

Plant, root, and soil microbiome

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system – Karthik Anantharaman – Nature Communications

Press: New Bacteria Groups, and Stunning Diversity, Discovered Underground
Berkeley Lab and UC Berkeley research also provides new clues about the roles of subsurface microbes in globally important cycles– Dan Krotz – Berkeley Lab

Plant microbiomes and sustainable agriculture. Deciphering the plant microbiome and its role in nutrient supply and plant immunity has great potential to reduce the use of fertilizers and biocides in agriculture – Philip Hunter – EMBO Reports

Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica – Sean T. S. Wei – Frontiers in Microbiology

Water microbiome

Seasonality of Coliform Bacteria Detection Rates in New Jersey Domestic Wells – Thomas B. Atherholt – Groundwater

Distinct factors shape aquatic and sedimentary microbial community structures in the lakes of western China – Jian Yang – Frontiers in Microbiology

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation – Jillian M. Petersen – Nature Microbiology

Press: ‘Farming’ bacteria to boost growth in the oceans – EurekAlert

Food microbiology

Different flour microbial communities drive to sourdoughs characterized by diverse bacterial strains and free amino acid profiles – Guiseppe Celano – Frontiers in Microbiology

Proteomics

Proteomics of Microbial Human pathogens – Nelson C. Soares – Frontiers in Microbiology

Techniques

Impact of Different Fecal Processing Methods on Assessments of Bacterial Diversity in the Human Intestine – Yu-Hsin Hsieh – Frontiers in Microbiology

Microbes in the news

Google doodle honors van Leeuwenhoek, father of microbiology– Steven Musil – CNET

HT: Ian Brooks. Podcast: Microbes, Genes and Human Endeavour: Ed Yong seeks to expand our understanding of microscopic microbes – BBC

Call for submissions: Kavli microbiome ideas challenge – Joanna Urban – ASM

#BacteriaHysteria

Dogs Licking Humans Can Be Dangerous; Transmission of Bacteria, Viruses Possible – Nature World News

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

SF Bay Area Microbiome Meetup

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With so many great Bay Area universities and life science companies working on the human microbiome and other microbial communities, the four of us (see below) thought it would make sense to organize a “Bay Area Microbiome Meetup”. This will – hopefully! – be the start of a series of get-togethers to connect, discuss, and share about the latest microbiome research.

IndieBio, a biotech accelerator located in San Francisco has graciously offered to host the event on Monday November 7, 2016, from 6-9 pm. The theme of this evening will be “Commercializing the microbiome”

The main purpose of our first event will be to get to know each other. We will host microbiome professionals from leading Bay Area research institutions (e.g., UCSF, UC Berkeley, UC Davis, and Stanford) as well as cutting edge life science and biotech organizations.

We will start the evening with a series of short pitches by representatives from several Bay Area microbiome companies and start-ups, followed by a Q&A panel. But most of the evening will be a mixer in an informal setting with food and drinks. This will be a great opportunity to strengthen the connections between microbiome scientists working in academia and biotech, and to learn, socialize, and network.

The event will be free, and drinks and light food will be provided, thanks to generous donations by Second Genome, Assembly Biosciences, One Codex, uBiome, Whole Biome, Osel Inc, and our host IndieBio. Seating is limited.

You can sign up for this event here: bay-area-microbiome-meetup.eventbrite.com

Here is a flyer to forward to other people who might be interested:  november-microbiome-meetup-v4 (PDF).

We hope this Microbiome Meetup will be a great success!

Jun Axup, IndieBio (our host)
Stephen Martis, UC Berkeley (poster design)
George Roche, UC Berkeley
Elisabeth Bik, Stanford University

 

 

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