November 28, 2015

Happy Thanksgiving, everyone! NCBI’s Pubmed nor Google Alerts did not take any holiday, so here is a post stuffed (pun intended) with new papers. For today, I got the microbiome of turkey, red wine, and coprolites. And strain-level variation in human-associated bacteria, cat periodontitis, and historical penguin activity too!

General microbiome

Nurturing the microbiome field: It is exciting to see the nucleus of a grand vision for the field, but we must make the fundamentals of the scientific method central to our mission – Pat Schloss – Science

Book: Microbial Endocrinology: Interkingdom Signaling in Infectious Disease and Health
Chapters include:

Pregnancy and birth

Preterm gut microbiota and metabolome following discharge from intensive care – Christopher J. Stewart – Scientific Reports

The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study – Toxicology Letters

Assessing the Intestinal Microbiota in the SHINE Trial – Ethan K. Gough – Clinical Infectious Diseases

Gravidas with Class III Obesity: Evaluating the Abdominal Skin Microbiota Above and Below the Panniculus – Rodney K Edwards – The Journal of Maternal-Fetal & Neonatal Medicine
Review: A Review of Antibiotic Use in Pregnancy – P. Brandon Bookstaver – Pharmacotherapy

Review: On the origin of species: Factors shaping the establishment of infant’s gut microbiota – Niels van Best – Birth Defects Research Part C: Embryo Today: Reviews

Review: Molecular characterization of the human microbiome from a reproductive perspective – Amir Mor – Fertility and Sterility

Review: Reproductive tract microbiome in assisted reproductive technologies – Jason M. Franasiak – Fertility and Sterility

Review: Gynecologic health and disease in relation to the microbiome of the female reproductive tract – Katherine A. Green – Fertility and Sterility

Human skin microbiome

Genetic associations and shared environmental effects on the skin microbiome of Korean twins – Jiyeon Si – BMC Genomics

Human respiratory microbiome

The Sputum Microbiome in Chronic Obstructive Pulmonary Disease Exacerbations
Yvonne J. Huang – Annals of the American Thoracic Society

Review: Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? – Fiona J. Whelan – Annals of the American Thoracic Society

Human oral microbiome

Microbiome of titanium and zirconia dental implants abutments – Cássio do Nascimento – Dental Materials

Human gut microbiome

Microbiota and food residues including possible evidence of pre-mammalian hair in Upper Permian coprolites from Russia – Piotr Bajdek – Lethaia

Red wine polyphenols modulate fecal microbiota and reduce markers of the metabolic syndrome in obese patients – Moreno-Indias Isabel – Food & Function

The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism – María V. Selma – Food & Function

The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota – Jérôme Boursier – Hepatology

Differences of microbiota in small bowel and faeces between irritable bowel syndrome patients and healthy subjects – Chen-Shuan Chung – Scandinavian Journal of Gastroenterology

Methodology, Not Concept of Fecal Microbiota Transplantation, Affects Clinical Findings – Bota Cui – Gastroenterology

The Gut-Liver Axis in Primary Sclerosing Cholangitis – Bertus Eksteen – Clinics in Liver Disease

Animal models

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science

Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota – Peris Mumbi Munyaka – PLOS ONE

Metabolomic study on the faecal extracts of atherosclerosis mice and its application in a Traditional Chinese Medicine – Feng Tian – Journal of Chromatography B

Animal microbiome

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment – Jessica L. Danzeisen – Frontiers in Veterinary Science

A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis – Stephen Harris – PLOS ONE

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species – Katherine R. Amato – Oecologia

Plant, root, and soil microbiome

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile – Renbin Zhu – Scientific Reports

Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function – Anna R. Peschel – Ecology

Effect of soil salinity and nutrient levels on the community structure of the root-associated bacteria of the facultative halophyte, Tamarix ramosissima, in southwestern United States – Takeshi Taniguchi – Journal of General and Applied Microbiology

Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots – Bao-Yu Tia – Scientific Reports

Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research

Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants – Amélia Bourceret – PLOS ONE

Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control – Marco Andreolli – Microbiological Research

Review: Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants – Charles W. Bacon – Symbiosis

Review: Culture-independent discovery of natural products from soil metagenomes – Micah Katz – Journal of Industrial Microbiology & Biotechnology

Built environment microbiology

ISS: Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Food microbiology

Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods – Eduardo Medina – Journal of Food Science

Microbial Ecology

Complete nitrification by Nitrospira bacteria – Holger Daims – Nature

Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science

Metagenomics and bioinformatics

Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria – Stephen Nayfach – BioRxiv

Techniques

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi – Kevin V. Solomon – Anaerobe

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies – Rashmi Sinha – Cancer Epidemiology, Biomarkers & Prevention

Microbes in the news

Is Double-Dipping Okay? CFUs in 4 types of dips after double dipping – Digg

New Research Reveals Bacteria Associated With Feline Gum Disease for the First Time – PR Newswire

Mission space food: Sugar-growing bacteria go into orbit – Clare Wilson – New Scientist

Your Coffee Machine Is a Breeding Ground for Caffeine-Resistant Bacteria – Matthew Braga – Motherboard

Your Poop Knows Best–New Study Shows Microbiome Can Help Predict Health Responses to Certain Foods – Patrick Mustain – Scientific American

Science, publishing, and career

China pursues fraudsters in science publishing – Mara Hvistendahl – Science
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November 25, 2015 – another digest

Posted on November 25, 2015 by eliesbik

Two digests today, to catch up with all literature that came out earlier this week. Gut microbiota of patients with stroke or TIAs, symbiosis within symbiosis, the coffee-machine microbiome, and chocolate making with yeasts.

Human gut microbiome

Dysbiosis of Gut Microbiota With Reduced Trimethylamine‐N‐Oxide Level in Patients With Large‐Artery Atherosclerotic Stroke or Transient Ischemic Attack – Jia Yin – Journal of the American Heart Association

Siri, What Should I Eat? – Reiner Jumpertz von Schwartzenberg, Peter J. Turnbaugh – Cell

Human skin microbiome

Microbiologic Safety of the Transareolar Approach in Breast Augmentation – Dana Mihaela Jianu – Aesthetic Surgery Journal

Microbiome models

Microbiota’s No Wasting Policy – Miguel P. Soares – Cell

Animal microbiome

Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis
Mateus Laguardia-Nascimento – PLOS ONE

Review: The natural occurrence of secondary bacterial symbionts in aphids – Sharon E. Zytynska – Ecological Entomology

Plant, root, and soil microbiome

Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts
Philippe Remigi – Trends in Microbiology

Soil microbial response to tetracycline in two different soils amended with cow manure – Luigi Chessa – Environmental Science and Pollution Research

Reviews: Friends or foes? Emerging insights from fungal interactions with plants – Susanne Zeilinger – FEMS Microbiology Reviews

Review: Extinction risk of soil biota – worrying paucity of existing information – Stavros D. Veresoglou – Nature Communications

Extremophile microbiome

Integrated ‘Omics’, Targeted Metabolite and Single-cell Analyses of Arctic Snow Algae Functionality and Adaptability – Stefanie Lutz – Frontiers in Microbiology

Water microbiome

Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Built environment microbiome

The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach – Cristina Vilanova – Scientific Reports

Food microbiology

Tuning chocolate flavor through development of thermotolerant Saccharomyces cerevisiae starter cultures with increased acetate ester production – Esther Meersman – Applied and Environmental Microbiology

Microbial genomes and ecology

Migration and horizontal gene transfer divide microbial genomes into multiple niches –
Rene Niehus – Nature Communications

The Good, the Bad, and the Tiny: A Simple, Mechanistic-Probabilistic Model of Virus-Nutrient Colimitation in Microbes – B. B. Cael – PLOS ONE

Microbes are trophic analogs of animals – Shawn A. Steffan – PNAS

Animal–microbe interactions and the evolution of nervous systems – Heather L. Eisthen – Philosophical Transactions B

Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi – Martin Ryberg – Molecular Ecology

Review: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome – Maayan Levy – Genome Medicine

Metagenomics and bioinformatics

Large-scale Machine Learning for Metagenomics Sequence Classification – Kévin Vervier – Bioinformatics

Techniques

Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing – Marcia L. Hart – PLOS ONE

Bacteria in the news

Your gut bacteria are controlling your appetite, study finds – Bec Crew – ScienceAlert

Beastly bacteria on extinct ancient carcasses offers ‘cure’ for modern oil pollution – Vera Salnitskaya – The Siberian Times

This ‘Plant Lamp’ uses bacteria to generate electricity – Sean Buckley – EnGadget
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November 21, 2015

Posted on November 21, 2015 by eliesbik

Human respiratory microbiome

Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation – Sang Hu Kim – PLOS Pathogens

Human gut microbiome

Review: Immune Interactions with Pathogenic and Commensal Fungi: A Two-Way Street – David M. Underhill – Immunity

Animal and other models

A Wave of Regulatory T Cells into Neonatal Skin Mediates Tolerance to Commensal Microbes – Tiffany C. Scharschmidt – Immunity

Animal microbiome

Spatial Variation of the Gut Microbiota in Broiler Chickens as Affected by Dietary Available Phosphorus and Assessed by T-RFLP Analysis and 454 Pyrosequencing – Maren Witzig – PLOS ONE

Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama – Cole G. Easson – PeerJ

Water microbiome

Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea – Meng Li – Nature Communications

Built environment microbiology

Fungal compositions and diversities on indoor surfaces with visible mold growths in residential buildings in the Seoul Capital Area of South Korea – C. An – Indoor Air

Characterization of Microbial Communities in Household Washing Machines – Ilka D. Nix – Tenside Surfactants Detergents

Metagenomics and Bioinformatics
DUDE-Seq: Fast Universal Denoising of Nucleotide Sequences – Byunghan Lee – ArXiv

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads – Xiao Zhu – BMC Bioinformatics

Viruses and phages

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing – Donatien F. Chedom – PLOS Computational Biology

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity – Magdalena Calusinska – Environmental Microbiology

Microbes in the news

Entering the Natural Antibiotic Arms Race – Anne Estes – Mostly Microbes

This Synthetic Bio Company Is Hacking Microbes to Build the Smells of the Future – Britt Wray – Motherboard

U of T researchers discover mysterious fungus that defends against neighbouring bacteria – News Medical

The Secret is Out! Review of “The Secret World Inside You” at the American Museum of Natural History in New York. – Anne Estes – Mostly Microbes

Innovative microbiome technology may help fight certain infections – News Medical

Science, publication, and career

America’s science legacy – Neil deGrasse Tyson – Science

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November 19, 2015

Posted on November 19, 2015 by eliesbik

Fungal dysbiosis in Crohn’s disease, a vagina monologue, stool sample storage, giraffe poop, Yellowstone lake, and extraction of bacteriophages.

Pregnancy and birth

Helminth infection, fecundity, and age of first pregnancy in women – Aaron D. Blackwell – Science

A Vagina Monologue: Mom’s Stress, Bugs, and Baby’s Brain – William A. Banks – Endocrinology

Human respiratory microbiome

The sinonasal bacterial microbiome in health and disease – Vijay R. Ramakrishnan – Current Opinion in Otolaryngology & Head & Neck Surgery

Human vaginal microbiome

Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity – A. Mitra – Scientific Reports

Human urinary tract microbiome

Role of the Gut Microbiome in Uremia: A Potential Therapeutic Target – Ali Ramezani – American Journal of Kidney Diseases

Human gut microbiome

Fungal dysbiosis in mucosa-associated microbiota of Crohn’s disease patients –
Giuseppina Liguori – Journal of Crohn’s and Colitis

Celiac Disease Genomic, Environmental, Microbiome, and Metabolomic (CDGEMM) Study Design: Approach to the Future of Personalized Prevention of Celiac Disease – Maureen M. Leonard – Nutrients

Sample storage conditions significantly influence faecal microbiome profiles – Jocelyn M Choo – Scientific Reports

Analysis of the Bacterial Diversity in Liver Abscess: Differences between
Pyogenic and Amoebic Abscesses – Miriam E. Reyna-Fabian – Am J Trop Med Hyg

Review: Gut microbiota regulates key modulators of social behavior – Arun Parashar – European Neuropsychopharmacology

Review: Metabolomic insights into the intricate gut microbial–host interaction in the development of obesity and type 2 diabetes – Magali Palau-Rodriguez – Frontiers in Microbiology

Animal models

The effect of microbial colonization on the host proteome varies by gastrointestinal location – Joshua S Lichtman – The ISME Journal

Animal microbiome

Analysis of the distal gut bacterial community by 454-pyrosequencing in captive giraffes (Giraffa camelopardalis) – Ousama AlZahal – Zoo Biology

Panamanian frog species host unique skin bacterial communities – Lisa K. Belden – Frontiers in Microbiology

Climate change stressors destabilize the microbiome of the Caribbean barrel sponge, Xestospongia muta – Michael P. Lesser – Journal of Experimental Marine Biology and Ecology

Plant, root, and soil microbiome

Bacteria in a wood fungal disease: characterization of bacterial communities in wood tissues of esca-foliar symptomatic and asymptomatic grapevines – Emilie Bruez – Frontiers in Microbiology

Water and extremophile microbiome

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China – Qiufang Zhang – Frontiers in Microbiology

Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools – Hyunmin Koo – Journal of Microbiological Methods

Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function – William P. Inskeep – Frontiers in Microbiology

Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica – Tom O. Delmont – Frontiers in Microbiology

Book Chapter: Microbiological Monitoring of Lake Baikal – Valentina V. Parfenova – Novel Methods for Monitoring and Managing Land and Water Resources in Siberia

Waste microbiology

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils – Silvena Boteva – Environmental Science and Pollution Research

Seasonal Changes in Bacterial Communities Cause Foaming in a Wastewater Treatment Plant – Ping Wang – Microbial Ecology

Temporal–spatial variation of bacterial diversity in estuary sediments in the south of Zhejiang Province, China – Xiao-Ming Lu – Applied Microbiology and Biotechnology

Viruses, metagenomics and bioinformatics

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut – Josué L. Castro-Mejía – Microbiome

Comparison of Illumina de novo assembled and Sanger sequenced viral genomes: A case study for RNA viruses recovered from the plant pathogenic fungus Sclerotinia sclerotiorum – Mahmoud E. Khalifa – Virus Research

ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens – David Bonsall – F1000 Research

More microbiology

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study – Yi-Yun Liu – The Lancet Infectious Diseases

Microbes in the news

Seafloor communities create electricity. In the digital age, we’re all connected by electricity — and some microbes are too – Meghan Bartels – ScienceLine

Microbe cheerleader: interview with Richard Roberts – Gijsbert Werner – Nature
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November 17, 2015

Posted on November 17, 2015 by eliesbik

Detecting bacteriophage DNA in mummies, microbiome depletion reduces obesity (in mice), viruses in city rats, microbes in alkaline hotsprings and in glaciers.

Events

European Microbiome Congress 2015: 18-19 November 2015, London.

Human respiratory tract microbiome

Viral aetiology of common colds of outpatient children at primary care level and the use of antibiotics – Janete Kamikawa – Mem. Inst. Oswaldo Cruz

Human reproductive tract microbiome

A DNA tool for early detection of vaginal dysbiosis in African women – Vicky Jespers – Research in Microbiology

Human gut microbiome

Natural mummification of the human gut preserves bacteriophage DNA – Tasha M. Santiago-Rodriguez – FEMS Microbiology Letters

Review: Inhibition of methanogenic archaea by statinsas a targeted management strategy for constipation andrelated disorders – K. Gottlieb

Review: Role of the Gut Microbiome in Uremia: A Potential Therapeutic Target – Ali Ramezani – American Journal of Kidney Diseases

Opinion: The Microbiome and Cancer: Is the ‘Oncobiome’ Mirage Real? – Ryan M. Thomas – Trends in Cancer

Review: The effect of gut microbiota on drug metabolism – Mi Jeong Kang – Expert Opinion on Drug Metabolism & Toxicology

Animal and bioreactor models

Microbiota depletion promotes browning of white adipose tissue and reduces obesity –
Nicolas Suárez-Zamorano – Nature Medicine

Variable responses of human and non-human primate gut microbiomes to a Western diet –
Katherine R. Amato – Microbiome

Research Highlight: Commensal bacterium prevents wasting – Cláudio Nunes-Alves – Nature Reviews Microbiology

Impact of a probiotic, inulin, or their combination on the piglets’ microbiota at different intestinal locations – V.A. Sattler – Beneficial Microbes

Iron Modulates Butyrate Production by a Child Gut Microbiota In Vitro – Alexandra Dostal – mBio

Research Hightlight: Scaling up spatial imaging of the gut microbiota – Naomi Attar – Nature Reviews Microbiology

Metagenomic analysis of anammox communities in three different microbial aggregates – Jianhua Guo – Environmental Microbiology

Microbial community analysis of a full-scale DEMON bioreactor – Alejandro Gonzalez-Martinez – Bioprocess and Biosystems Engineering

Re-appraisal of the phylogeny and fluorescence in situ hybridization probes for the analysis of the Competibacteraceae in wastewater treatment systems – Simon J. McIlroy – Environmental Microbiology Reports

Animal microbiome

New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics – Thomas Arn Hansen – PLOS ONE

Bleaching of Baikalian sponge affects the taxonomic composition of symbiotic microorganisms – O. V. Kaluzhnaya – Russian Journal of Genetics

Experimental Infection of Snakes with Ophidiomyces ophiodiicola Causes Pathological Changes That Typify Snake Fungal Disease – Jeffrey M. Lorch – mBio

Plant, root, and soil microbiome

Glyphosate effects on soil rhizosphere-associated bacterial communities – Molli M. Newman – Science of the Total Environment

Soil microarthropods support ecosystem productivity and soil C accrual: Evidence from a litter decomposition study in the tallgrass prairie – Jennifer L. Soong – Soil Biology and Biochemistry

Microbial communities and organic matter composition in surface and subsurface sediments of the Helgoland mud area, North Sea – Oluwatobi E. Oni – Frontiers in Microbiology

Shifts in the composition and potential functions of soil microbial communities responding to a no-tillage practice and bagasse mulching on a sugarcane plantation – Toshiko Miura – Biology and Fertility of Soils

Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands, and scrub biome – Andrey M. Yurkov – FEMS Yeast Research

Coal mining practices reduce the microbial biomass, richness and diversity of soil –
Patricia Dorr de Quadros – Applied Soil Ecology

Water microbiome

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities – Zilian Zhang – PLOS ONE

Comparative study on composition and abundance of major planktons and physico-chemical characteristics among two ponds and Lake Tana, Ethiopia – Wondie Zelalem Amanu – Journal of Coastal Life Medicine

Extremophile microbiome

Metagenomics of an alkaline hot spring in Galicia (Spain): microbial diversity analysis and screening for novel lipolytic enzymes – Olalla López-López – Frontiers in Microbiology

Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic – Purnima Singh – Journal of Basic Microbiology

Built environment microbiology

Microbiota formed on attached stainless steel coupons correlate with the natural biofilm of the sink surface in domestic kitchens – Birgitte Moen – Canadian Journal of Microbiology

Towards an antimicrobial ‘microglove’ – Ewoud Reilman – Scientific Reports

Infection microbiology

Research Highlight: The Origin of a Killer Revealed by Bronze Age Yersinia Genomes – Shijulal Nelson-Sathi – Cell Host & Microbe

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago – Simon Rasmussen – Cell

Review: The Black Death: Its origin and routes of dissemination – Kristina Lenz – Scandinavian Journal of History

Review: Emerging methodologies for pathogen identification in positive blood culture testing – Grégory Dubourg – Expert Review of Molecular Diagnostics

Microbial ecology

Integrating ecological and engineering concepts of resilience in microbial communities – Hyun-Seob Song – Frontiers in Microbiology

Perspective: Rethinking “mutualism” in diverse host-symbiont communities – Alexandra A. Mushegian – BioEssays

Techniques

Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community – Yang Lu – PLOS ONE

Bioinformatics, viruses, and metagenomics

The State of Software in Evolutionary Biology: code quality of 15 highly cited tools – Diego Darriba – bioRxiv

Kaiju: Fast and sensitive taxonomic classification for metagenomics – Peter Menzel – bioRxiv

A novel group of diverse Polinton-like viruses discovered by metagenome analysis – Natalya Yutin – BMC Biology

Microbes in the news

Taking Antibiotics Can Change the Gut Microbiome for Up to a Year. A new study illuminates the problems antibiotic overuse could cause for individual patients – Julie Beck – The Atlantic

Health Experts Are Explaining Drug-Resistant Bacteria Poorly: Their confusing jargon is pushing people toward bad decisions – Ed Yong – The Atlantic

5 Common Myths About Antibiotic-Resistant Bacteria – Alexandra Sifferlin – Time

There’s Life in Rocks Deep Below the Sea Floor. Seriously. – Heather Goldstone – Cape and Islands

More armadillos that carry leprosy bacteria found in Southern US – Amanda Lane – Midday Daily

Blood-Gut Barrier. Scientists identify a barrier in mice between the intestine and its blood supply, and suggest how Salmonella sneaks through it – Ruth Williams – The Scientist

Microbes Play Role in Anti-Tumor Response
Gut microbiome composition can influence the effectiveness of cancer immunotherapy in mice – Anna Azvolinsky – The Scientist

How depleting the gut microbiota protects from obesity – MedicalXpress

A Complex Disorder. Factors that likely contribute to obesity include disruptions to intercellular signaling, increased inflammation, and changes to the gut microbiome – Stephen D. Hursting – The Scientist

Effect of feed on microbiota balance in piglets – All About Feed

Skin Must Develop Tolerance to ‘Good’ Bacteria Early In Life, Says New Study: Research Probes How Skin’s Resident Communities of Microbes Are Established – Pete Farley – University of California San Francisco

How You’re Born May Affect Your Brain Development – Stephanie Pappas – Brain Decoder

Bacteria Hysteria

Doctors say to watch out for bacteria in your makeup bag – NBC News

Proper Use Of Wipes Kills Germs, Improper Use Could Spread Them – Maria Simbra – CBS Local

Microbiology and Art

What Lives on the Subway Pole? – Jen Kirby – New York Magazine

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November 14, 2015

Posted on November 14, 2015 by eliesbik

A paper from our lab(s) on inbred mouse strain gut microbiota variation, bacteria reduce fungi on toads, 20 years of bacterial genome sequencing, and 100 years of phage research.

Jobs

Tenure Track Position in Microbial Metagenomics – Texas Tech University in Lubbock, TX

Human oral microbiome

In Vitro Culture of Previously Uncultured Oral Bacterial Phylotypes – Hayley Thompson – Applied and Environmental Microbiology

Oral microbiome in chinese patients with aggressive periodontitis and their family members – Yi Li – Journal of Clinical Periodontology

Human gut microbiome

Probiotic supplementation influences faecal short chain fatty acids in infants at high risk for eczema – H.K. Kim – Beneficial Microbes

Review: Establishing a causal link between gut microbes, body weight gain and glucose metabolism in humans – towards treatment with probiotics – L.K. Stenman – Beneficial Microbes

Review: An Integrated Outlook on the Metagenome and Metabolome of Intestinal Diseases – Wanping Aw – Diseases

Animal models

I’m a co-author: Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time – Yana Emmy Hoy – PLOS ONE

Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice – Marc Schneeberger – Scientific Reports

Effect of Clostridium perfringens infection and antibiotic administration on microbiota in the small intestine of broiler chickens – Yewande O. Fasina – Poultry Science

Host genetic control of the microbiota mediates Drosophila nutritional phenotype – John M. Chaston – Applied and Environmental Microbiology

Bromochloromethane, a methane analogue, affects the gut microbiota and metabolic profiles of the rat gastrointestinal tract – Yu-Xiang Yang – Applied and Environmental Microbiology

Animal microbiome

Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas) – Jordan G Kueneman – The ISME Journal

Leptospira and Bats: Story of an Emerging Friendship – Muriel Dietrich – PLOS Pathogens

Intraspecific variation in microbial symbiont communities of the sun sponge, Hymeniacidon heliophila, from intertidal and subtidal habitats – Brooke L. Weigel – Applied and Environmental Microbiology

Successive shifts in the microbial community of the surface mucus layer and tissues of the coral Acropora muricata under thermal stress – Sonny T.M. Lee – FEMS Microbiology Ecology

Invasive ants carry novel viruses in their new range and form reservoirs for a honeybee pathogen – Alexandra Sébastien – Biology Letters

Plant, root, and soil microbiome

Proteomic Analysis of Microbial Community Inhabiting Asian Dust Source Region – Simranjeet Singh Sekhon – CLEAN – Soil, Air, Water

Landscape Position Influences Microbial Composition and Function via Redistribution of Soil Water across a Watershed – Zhe Du – Applied and Environmental Microbiology

Common foliar fungi of Populus trichocarpa modify Melampsora rust disease severity – Posy E. Busby – New Phytologist

Cave microbial community composition in oceanic islands: disentangling the effect of different colored mats in diversity patterns of Azorean lava caves – Cristina Riquelme – FEMS Microbiology Ecology

Mini-review: Lichens as natural sources of biotechnologically relevant bacteria – Marcelino T. Suzuki – Applied Microbiology and Biotechnology

Water / extremophile microbiome

Single Cells within the Puerto Rico Trench Suggest Hadal Adaptation of Microbial Lineages – Rosa León-Zayas – Applied and Environmental Microbiology

Cyanobacterial community composition in Arctic soil crusts at different stages of development – Ekaterina Pushkareva – FEMS Microbiology Ecology

Effects of Volcanic Pumice Inputs on Microbial Community Composition and Dissolved C/P Ratios in Lake Waters: an Experimental Approach – B. E. Modenutti – Microbial Ecology

Phages and viruses

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi – L. Nerva – Virus Research

Review: A century of the phage: past, present and future – George P. C. Salmond & Peter C. Fineran – Nature Reviews Microbiology

Genome sequencing and metagenomics

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification – Kirsten A. Ziesemer – Scientific Reports

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes – Stephen Nayfach – PLOS Computational Biology

SONEC: Metabolic Network-Guided Binning of Metagenomic Sequence Fragments – Matthew B. Biggs – Bioinformatics

Decreases in average bacterial community rRNA operon copy number during succession – Diana R Nemergut – The ISME Journal

Review: Twenty years of bacterial genome sequencing – Nicholas J. Loman & Mark J. Pallen – Nature Reviews Microbiology

Techniques

Community-Level Physiological Profiling of Microbial Communities in Constructed Wetlands: Effects of Sample Preparation – Mark Button – Applied Biochemistry and Biotechnology

Microbes in the news

Your Gut May Be Home To An Entirely New Form Of Life – Maddie Stone – Gizmodo

Growth Rate of Gut Bacteria Related to Specific Diseases – Rachel Lutz – HCP Live

Sweaty feet, stinky cheese, and the microbiome – Matt McCarthy – STAT

Parasitic fungi and the battle against coffee rust disease – Jim Erickson – University of Michigan

Body’s Microorganisms Could Keep Humans More Healthy – Gene Marcial – Forbes

Not creepy at all! 13 creepy pictures of the microbes that are living inside of you – Julia Calderone – Tech Insider

You’ve been fighting morning breath all wrong – Lydia Ramsey – Business Insider Australia

Bacteria-Infused Material Pulls Energy Out of Poop – But don’t get too excited, because this poop battery is terribly inefficient – William Herkewitz – Popular Mechanics

This Little Bot Walks on Water and Runs on Bacteria – Maddie Stone – Gizmodo

Why do potatoes grow pink slime? Clostridium puniceum could fight MRSA – Alexandra Sarabia – PBS NewsHour

Bacteria Hysteria

Your Unwashed Bras Are Growing (Mostly Harmless) Bacteria – Beth Skwarecki – LifeHacker

November 13, 2015

Posted on November 13, 2015 by eliesbik

Happy Friday the 13th! Today’s post features a gut-vascular barrier implicated in celiac disease, bison microbiota, 16S rRNA genes in metagenomics data, soil communities at neighboring sites, enriching microbial DNA, and lots of gut microbiota reviews.

Human gut microbiome

(humans and animal models; celiac disease) A gut-vascular barrier controls the systemic dissemination of bacteria – Ilaria Spadoni – Science

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella – Petia Kovatcheva-Datchary – Cell Metabolism

Effect of Antibiotics on Gut Microbiota, Gut Hormones and Glucose Metabolism – Kristian H. Mikkelsen – PLOS ONE

Review: The Enteric Microbiome in Hepatobiliary Health and Disease – James H. Tabibian – Liver International

Review: Microbiota and aging – Stephan C Bischoff – Current Opinion in Clinical Nutrition & Metabolic Care

Review: The impact of gut microbiota on brain and behaviour: implications for psychiatry – Timothy G Dinan – Current Opinion in Clinical Nutrition & Metabolic Care

Review: The gut microbiota keeps enteric glial cells on the move; prospective roles of the gut epithelium and immune system – Panagiotis S. Kabouridis – Gut Microbes

Review: The joint power of sex and stress to modulate brain–gut–microbiota axis and intestinal barrier homeostasis: implications for irritable bowel syndrome – M. Pigrau – Neurogastroenterology & Motility

Review: Microbiome and Health in Past and Present Human Populations – Christina Warinner – American Anthropologist

Animal and bioreactor models

Individual Members of the Microbiota Disproportionately Modulate Host Innate Immune Responses – Annah S. Rolig – Cell Host & Microbe

Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon – Sophie Fehlbaum – PLOS ONE

Animal microbiome

Seasonal Shifts in Diet and Gut Microbiota of the American Bison (Bison bison) – Gaddy T. Bergmann – PLOS ONE

Fecal contamination of echinoderms: first report of heavy E. coli loading of sea urchins from a natural growing area – M Bouchoucha – Letters in Applied Microbiology

Plant, root, and soil microbiome

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites – A. L. Gagliano – GeoBiology

Soil microorganisms behave like macroscopic organisms: patterns in the global distribution of soil euglyphid testate amoebae – Enrique Lara – Journal of Biogeography

Arsenic uptake, arsenite efflux and plant growth in hyperaccumulator Pteris vittata: Role of arsenic-resistant bacteria – Yong-He Han – Chemosphere

Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea – Hanin Alzubaidy – Gene

Review: Current trends in Bt crops and their fate on associated microbial community dynamics: a review – Amit Kishore Singh – Protoplasma

Built environment and waste treatment

Separate treatment of hospital and urban wastewaters: A real scale comparison of effluents and their effect on microbial communities – Teofana Chonova – Science of the Total Environment

Bioinformatics and metagenomics

Introducing REAGO: Reconstructing 16S rRNA genes in metagenomic data – Cheng Yuan – Bioinformatics

Techniques
Enriching microbial DNA: Changes in 16s RNA Gene Microbial Community Profiling by Concentration of Prokaryotic DNA – Angela Glassing – Journal of Microbiological Methods

The Sequence of Sequencers: The History of Sequencing DNA – James M. Heather – Genomics

Microbes in the news

Water Quality in Green Buildings – Katherine Dahlhausen – MicroBEnet

Video: Jonathan Eisen: Microbes in Food and Agriculture: Dr. Jonathan Eisen speaking at UC Davis’s Institute for Food and Ag Literacy round table about the impact the microbiome has made and potential relevance in health, food, and agriculture.

Want a Stronger Defense System against Diseases? Add Some Worms – Sheena Faherty – Scientific American

From garden to gut: New book from UW’s David Montgomery explores an unfolding scientific revolution – Hannah Hickey – University of Washington

Video in Dutch: How many bacteria do you exchange during French Kissing? A demonstration by microbiologist Remco Kort

Bacteria and bacteriophages collude in the formation of clinically frustrating biofilms – Phys.org

Extreme bacteria live in odd corners of the ecosystem – North Country Public Radio

Bacteria Hysteria

Sponsored report: Bacteria, Fecal Matter Found in Rain Puddles on Ground

Science, publishing, and career

In the eye of the Twitterstorm: Social media is shaking up how scientists talk about gender issues – Lauren Morello – Nature
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November 12, 2015

Posted on November 12, 2015 by eliesbik

Gut microbiome and definition of self, symbionts of corals and algae, and microbial geobiology of space exploration. And – yeah! – my Twitter account made it to a “Top 100 Twitter Influencers Working in Life Sciences” list. My Twitter handle is @MicrobiomDigest.

Human gut microbiome

Extensive T-cell epitope repertoire sharing among human proteome, gastrointestinal microbiome, and pathogenic bacteria: implications for the definition of self –
Robert D. Bremel – Frontiers in Immunology

Gut microbiota and diet in patients with different glucose tolerance – Lilit Vanikovna Egshatyan – Endocrine Connections

Review: Alcoholic Liver Disease: The Gut Microbiome and Liver Cross Talk – Phillipp Hartmann – Alcoholism: Clinical and Experimental Research

Review: Linking Microbiota to Human Diseases: A Systems Biology Perspective – Hao Wu – Trends in Endocrinology & Metabolism

Review: Gut microbiota and host metabolism in liver cirrhosis – Makoto Usami – World Journal of Gastroenterology

Infection and cancer microbiology

Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis – Samuel A. Shelburne – PLOS ONE

Animal microbiome

Open Access: Stable and sporadic symbiotic communities of coral and algal holobionts – Eric R. Hester – The ISME Journal

Plant, root, and soil biology

Past water management affected GHG production and microbial community pattern in Italian rice paddy soils – A. Lagomarsino – Soil Biology and Biochemistry

Elemental stoichiometry indicates predominant influence of potassium and phosphorus limitation on arbuscular mycorrhizal symbiosis in acidic soil at high altitude –
Mohammad Haneef Khan – Journal of Plant Physiology

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach – P. Bhattacharyya – Science of The Total Environment

Food microbiology

Monitoring of spoilage and determination of microbial communities based on 16S rRNA gene sequence analysis of whole sea bream stored at various temperatures – Foteini F. Parlapani – LWT – Food Science and Technology

Variation in fungal microbiome (mycobiome) and aflatoxin in stored in-shell peanuts at four different areas of China – Ning Ding – Frontiers in Microbiology

Waste microbiology

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate – Lijuan Yan – Science of the Total Environment

Space microbiology

An ESA Roadmap for Geobiology in Space Exploration – Claire R Cousins – Acta Astronautica

Transcriptomics

Protocol: Prokaryotic Metatranscriptomics – Danilo Pérez-Pantoja – Springer Protocols Handbooks

Microbes in the news

Story behind the paper: Porphyrobacter mercurialis, a new species found by #citizenscience and then sent to the #iss – David Coil – MicroBEnet

Getting a flu shot every year? More may not be better – Helen Branswell – STAT news

Dangerous liaison: Bacteria, viruses in league – Bruce Goldman – Stanford Medicine News

Filamentous Bacteriophage Promote Biofilm Assembly and Function – Patrick R. Secor – Cell Host & Microbe

Intestinal Pathogens Change the Microbiome, Cause E. Coli To “Bloom” – Interview with Shannon D. Manning – Medical Research

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November 11, 2015

Posted on November 11, 2015 by eliesbik

Red-pigmented haloarchaea in flamingo feathers, cyanobacteria of the Western Himalaya, and read-filtering of HT amplicon reads.

Human respiratory microbiome

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention – Leah Cuthbertson – ISME Journal

Human reproductive tract microbiome

Genital tract colonization with Ureaplasma spp. and its association with abnormal vaginal flora – Ellen Vancutsem – Journal of Medical Microbiology

Impact of Bacterial Vaginosis on Perineal Tears during Delivery: A Prospective Cohort Study – Vincent Letouzey – PLOS ONE

Human gut microbiome

Carriage of enterobacteria producing extended spectrum beta-lactamases and composition of the gut microbiota in an Amerindian community – María José Gosalbes – Antimicrobial Agents and Chemotherapy

Animal microbiome (and archaea)

Occurrence of viable, red-pigmented haloarchaea in the plumage of captive flamingoes – Kyung June Yim – Scientific Reports

DGGE: Effect of chemical stress and ultraviolet radiation in the bacterial communities of zebrafish embryos – Jacinta M.M. Oliveira – Environmental Pollution

Plant, root, and soil microbiome

Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya – Kateřina Čapková – Microbial Ecology

Phytostabilization of moderate copper contaminated soils using co-inoculation of Vicia faba with plant growth promoting bacteria – Imen Challougui Fatnassi – Journal of Basic Microbiology

Effects of Common Mycorrhizal Network on Plant Carbohydrates and Soil Properties in Trifoliate Orange–White Clover Association – Ze-Zhi Zhang – PLOS ONE

Distributions and compositions of old and emerging flame retardants in the rhizosphere and non-rhizosphere soil in an e-waste contaminated area of South China – Shaorui Wang – Environmental Pollution

Water microbiome

High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling – Tomàs Llorens-Marès – Microbial Ecology

Bioinformatics

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences – Vinita Deshpande – Mycologia

A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies – Fernando Puente-Sánchez – Nucleic Acids Research

Microbes in the news

One course of antibiotics disrupts gut microbiome for a year – Medical News Today

Science, publishing, and career

Public Data Archiving in Ecology and Evolution: How Well Are We Doing? – Dominique G. Roche – PLOS Biology
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Microbiome Digest – Bik's Picks

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

Category Archives: Animal microbiome

November 28, 2015

November 26, 2015

November 25, 2015 – another digest

November 21, 2015

November 19, 2015

November 17, 2015

November 14, 2015

November 13, 2015

November 12, 2015

November 11, 2015