Category Archives: Microbes in the News

February 5, 2016

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Just a quick new Digest in the lunch break at the #GamingMetrics conference at UC Davis. Here is a Storify from Day 1 (yesterday) by Jonathan Eisen – more to follow soon.

Pregnancy and birth

Microbial transmission from mothers with obesity or diabetes to infants: an innovative opportunity to interrupt a vicious cycle – Taylor K. Soderborg – Diabetologia

Human urinary tract microbiome

16S rRNA gene-based metagenomic analysis reveals differences in bacteria-derived extracellular vesicles in the urine of pregnant and non-pregnant women – Jae Young Yoo – Experimental & Molecular Medicine

Human gut microbiome

Fungal microbiota dysbiosis in IBD – Harry Sokol – Gut

Animal models of microbiome research

Oxygen Affects Gut Bacterial Colonization and Metabolic Activities in a Gnotobiotic Cockroach Model – Dorothee Tegtmeier – Applied and Environmental Microbiology

Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches – Aram Mikaelyan – Applied and Environmental Microbiology

Associations of microbiota and toll-like receptor signaling pathway in esophageal adenocarcinoma – Ali H. Zaidi – BMC Cancer

Comparison of fecal microbiota between German Holstein dairy cows with and without left-sided displacement of the abomasum – Eun-Sik Song – Journal of Clinical Microbiology

Animal microbiome

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos – Felix Sommer – Cell Reports

Plant, root, and soil microbiome

Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India – Subramanya Rao – Indian Journal of Microbiology

Microbial communities play important roles in modulating paddy soil fertility
Xuesong Luo – Scientific Reports

Diversity of archaeal and bacterial communities on exfoliated sandstone from Portchester Castle (UK) – Elisabetta Zanardini – International Biodeterioration & Biodegradation

Distance from the sea as a driving force of microbial communities under water potential stresses in litters of two typical Mediterranean plant species – Anne Marie Farnet Da Silva – Geoderma

Opinion: Back to the future of soil metagenomics – Joseph Nesme – Frontiers in Microbiology

Waste and water treatment

Occurrence and enrichment of ‘bacterial sherpas’: climb to sustainability in wastewater treatment – M. Arnaldos – Water Science & Technology

Metagenomics

Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs – Francy Jimenez-Infante – Applied and Environmental Micro

Microbial Ecology

Model-based media selection to minimize the cost of metabolic cooperation in microbial eco-systems – Mattia Zampieri – Bioinformatics

Microbes in the news

Savvy bacteria parents distribute damage unevenly among their children – Cara Giaimo – Atlas Obscura

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February 4, 2016

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A late digest today – Meetings and lab work kept me busy all day! Review about gut microbiota and malnutrition, Helicobacter infection affects local microbiome, salinity tolerance in corals, rhizosphere reviews, microbial mats in Shark Bay, and missing CRISPR regions in major bacterial lineages.

Jobs

Assistant, Associate or Senior Editor (Microbiology and Infectious Disease), Nature Communications, London, New York or Shanghai

Bioinformatics Scientist, Microbiome – Synthetic Genomics, Inc. – La Jolla CA

Pregnancy and birth
Routine Amoxicillin for Uncomplicated Severe Acute Malnutrition in Children – Sheila Isanaka – New England Journal of Medicine

Review: The case in favour of probiotics before, during and after pregnancy: insights from the first 1,500 days – G. Reid – Beneficial Microbes

Review: Development of the Neonatal Intestinal Microbiome and Its Association With Necrotizing Enterocolitis – Timothy G. Elgin – Clinical Therapeutics

Human oral microbiome

Interesting choice of  journal: Periodontitis induced by Porphyromonas gingivalis drives periodontal microbiota dysbiosis and insulin resistance via an impaired adaptive immune response – Vincent Blasco-Baque

Non-oral gram-negative facultative rods in chronic periodontitis microbiota – Arie J. van Winkelhoff – Microbial Pathogenesis

Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis – S. Bizzarro – Scientific Reports

Human respiratory microbiome

Effect of Advanced HIV Infection on the Respiratory Microbiome – Homer L Twigg III – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The emerging view of Firmicutes as key fibre degraders in the human gut – David Berry – Environmental Microbiology

Review: Gut Microbiota and Malnutrition – Matthieu Million – Microbial Pathogenesis

Review: Diet, Microbiota, And Dysbiosis: A ‘Recipe’ For Colorectal Cancer – Kishore Vipperla – Food & Function

Review: Microbiota, Immunity and the Liver – T. Vaikunthanathan – Immunology Letters

Animal and other models of microbiome research

Alterations of the Ileal and Colonic Mucosal Microbiota in Canine Chronic Enteropathies – Eric Cassmann – PLOS ONE

In a Neonatal Piglet Model of Intestinal Failure, Administration of Antibiotics and Lack of Enteral Nutrition Have a Greater Impact on Intestinal Microflora Than Surgical Resection Alone – Crystal L. Levesque – Journal of Parenteral & Enteral Nutrition

Development of the Chick Microbiome: How Early Exposure Influences Future Microbial Diversity – Anne L. Ballou – Frontiers in Veterinary Science

Gastric Helicobacter pylori Infection Affects Local and Distant Microbial Populations and Host Responses – Sabine Kienesberger – Cell Reports

Salmonella enterica Serovar Typhimurium Exploits Inflammation to Modify Swine Intestinal Microbiota – Rosanna Drumo – Frontiers in Cellular and Infection Microbiology

Changes in intestinal microflora of Caenorhabditis elegans following Bacillus nematocida B16 infection – Qiuhong Niu – Scientific Reports

Chitosan lowers body weight through intestinal microbiota and reduces IL-17 expression via mTOR signalling – Dingfu Xiao – Journal of Functional Foods

The effect of agave fructan products on the activity and composition of the microbiota determined in a dynamic in vitro model of the human proximal large intestine – Marjorie E. Koenen – Journal of Functional Foods

Animal microbiome

Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome – Till Röthig – Molecular Ecology

High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet – Wen Wang – Microbiology Open

Plant, root, and soil microbiome

Spatial Distribution of Fungal Communities in an Arable Soil – Julia Moll – PLOS ONE

Soil Nitrogen Status Modifies Rice Root Response to Nematode-Bacteria Interactions in the Rhizosphere – Yanhong Cheng – PLOS ONE

Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria – Paul C. A. Wintermans – Plant Molecular Biology

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition – Cheng Wang – Biotechnology for Biofuels

Microbial Profiling of a Suppressiveness-Induced Agricultural Soil Amended with Composted Almond Shells – Carmen Vida – Frontiers in Microbiology

Editorial: How does the tree root microbiome assemble? Influence of ectomycorrhizal species on Pinus sylvestris root bacterial communities – Aurélie Deveau – Environmental Microbiology

Lots of reviews on the plant rhizosphere in Trends in Plant Science: 

Review: Impact of Bacterial–Fungal Interactions on the Colonization of the Endosphere – Leonard S. van Overbeek – Trends in Plant Science

Review: Signaling in the Rhizosphere – Vittorio Venturi – Trends in Plant Science

Review: Root–Root Interactions: Towards A Rhizosphere Framework – Liesje Mommer – Trends in Plant Science

Review: Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication – Nicole M. van Dam – Trends in Plant Science

Opinion: Mannitol in Plants, Fungi, and Plant–Fungal Interactions
Takshay K. Patel – Trends in Plant Science

Water and extremophile microbiome

Evolution of Chemical Characteristics of Technosols in an Afforested Coal Mine Dump over a 20-year Period – Ivana M. Rivas-Pérez – Land Degradation and Development

Microbial mats: New multi-scale perspectives on the stromatolites of Shark Bay, Western Australia – E. P. Suosaari – Scientific Reports

Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China – Peike Gao – Scientific Reports

Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) – Christina Pavloudi – Marine Genomics

Microbial diversity in European alpine permafrost and active layers – Beat Frey – FEMS Microbiology Ecology

Nutrient and metal pollution of the eastern Gulf of Finland coastline: Sediments, macroalgae, microbiota – Yulia Gubelit – Science of the Total Environment

Food microbiology

Unraveling the Enzymatic Basis of Wine “Flavorome”: A Phylo-Functional Study of Wine Related Yeast Species – Ignacio Belda – Frontiers in Microbiology

Developmental Peculiarities and Seed-Borne Endophytes in Quinoa: Omnipresent, Robust Bacilli Contribute to Plant Fitness – Andrea Pitzschke – Frontiers in Microbiology

Viruses, phages, and CRISPRs

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems – David Burstein – Nature Communications

High-Throughput Isolation of Giant Viruses in Liquid Medium Using Automated Flow Cytometry and Fluorescence Staining – Jacques Y. B. Khalil – Frontiers in Microbiology

Review: Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems – Mart Krupovic – Current Opinion in Microbiology

Techniques

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity – Laura S. Morris – Journal of Microbiological Methods

More microbiology

Elie Metchnikoff, the Man and the Myth – Gordon S. – Journal of Innate Immunology

Microbes in the news

What Your Low-Fiber Diet Does to Your Health – Mandy Oaklander – Time

Your beard doesn’t contain poop, but it could help develop new antibiotics – Sarah Kaplan – The Washington Post

Modern microbial ecosystems provide window to early life on Earth. UM Rosenstiel School-led team reveals new details on modern-day stromatolites – Science Daily

Two Santa Clara University Students Confirmed with Meningitis – ABC7

USDA Imposes Stricter Limit On Salmonella Bacteria In Poultry Products – NPR Morning Edition

Young scientists present intriguing and surprising research – Kristen Browning-Blas – Colorado State University

Meet the CEO of Europe’s Leading Microbiome Biotech, Pierre Belichard of Enterome – Labiotech

Podcast: As Arctic Permafrost Thaws, Microbes Kick Into Action – with Janet Jansson – Science Friday

Podcast: Bear Gut Microbes Help Prep Hibernation – Karen Hopkin – Scientific American

Podcast: The Good Side of Viruses – Medical Discovery News
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February 3, 2016

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Microbiome and risk for chemotherapy-induced colitis, fungal communities in boreal forest, and our new paper on marine mammal microbiotas!

Jobs and events

Postdoc in Metagenomics and Microbial Ecology – Linné Universitetet Kalmar, Sweden

General microbiome

Collection: The Human Microbiome – Cell Host & Microbe

Human gut microbiome

Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis – Krista Dubin – Nature Communications

Animal microbiome

My latest paper: Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea – Elisabeth M. Bik – Nature Communications

Plant, root, and soil microbiome

Experimental warming alters potential function of the fungal community in boreal forest – Kathleen K. Treseder – Global Change Biology

Microbes in the news

Stanford Researchers Uncover New Bacterial Diversity Inside U.S. Navy Dolphins – Steve Fyffe – Stanford CISAC

What makes Listeria deadly – Nature

Antibiotic-resistant bacteria thriving in Galway’s sewers – Thérèse Hannon – Connacht Tribune

Plush pandemic: Colossal microbes taking over the world. Interview with Drew Oliver, creator of Giant Microbes – Andrew Jermy

Altru microbiologists discover bacteria, name it ‘altruii’ – Jennifer Johnson – Grand Forks Herald

Antibiotic-Resistant Bacteria May Have Met Their Match – Sheila Foran – University of Connecticut

Fil-Am microbiology student receives scholar award at the 28th CSU Biotechnology Symposium – Asian Journal

Qiagen NV: New agreements underscore QIAGEN’s leadership in bioinformatics – The Wall Street Transcript

Science, publishing, and career

Reproducibility: A tragedy of errors – David B. Allison – Nature

Want to correct the scientific literature? Good luck – Alison McCook – Retraction Watch

Counselling: Knowledge is power: finding a mentor outside the lab – Paul Smaglik – Nature

Chicago Professor Resigns Amid Sexual Misconduct Investigation – Amy Harmon – New York Times

Bik’s Picks

The Weird Thing About Cat Legs – Ed Yong – The Atlantic

Doctors Rank Hazardous and Healthy Hospital Food Environments – Physicians Committee for Responsible Medicine
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February 2, 2016

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Events

Note: website was working yesterday, but not this morning. I hope to fix this soon. SCDA Workshop on Statistical and Algorithmic Challenges in Microbiome Data Analysis, Feb 25-26, New York

Pregnancy and birth microbiome

Not carefully worded, and not novel: New Insight into the Analysis of Amniotic Fluid Microflora using 16S rRNA Sequencing – Young-Ah You – JMM Case Reports

Human oral microbiome

Perspective: What Are We Learning and What Can We Learn from the Human Oral Microbiome Project? – Benjamin Cross – Current Oral Health Reports

Animal microbiome

Increasing the Richness of Culturable Arsenic-Tolerant Bacteria from Theonella swinhoei by Addition of Sponge Skeleton to the Growth Medium – Keren Ray – Microbial Ecology

Comparative studies of the composition of bacterial microbiota associated with the ruminal content, ruminal epithelium and in the faeces of lactating dairy cows –
Jun-hua Liu – Microbial Biotechnology

Experimental exposure to trace metals affects plumage bacterial community in the feral pigeon – M. Chatelain – Journal of Avian Biology

Plant, root, and soil microbiome

Effects of biogas and raw slurries on grass growth and soil microbial indices – Stefanie Wentzel – Journal of Plant Nutrition and Soil Science

Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression – Menno van der Voor – Ecology Letters

Impact of grassland management regimes on bacterial endophyte diversity differs with grass species – Franziska Wemheuer – Letters in Applied Microbiology

Novel soil fumigation method for suppressing cucumber Fusarium wilt disease associated with soil microflora alterations – Rong Li – Applied Soil Ecology

Water and extremophile microbiome

‘Candidatus Kryptonia’: Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs – Emiley A. Eloe-Fadrosh – Nature Communications

Novel Virophages Discovered in a Freshwater Lake in China – Chaowen Gong – Frontiers in Microbiology

Metagenomics and bioinformatics

Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken) – Fabiola Valenzuela-González – Journal of Microbiological Methods

Opinion: From barcodes to genomes: extending the concept of DNA barcoding – Eric Coissac – Molecular Ecology

More microbes

Streptomyces thermoautotrophicus does not fix nitrogen – Drew MacKellar – Scientific Reports

Microbes in the news

How to (not) write a microbiome grant, Part I by David Baltrus

Does Having a C-Section Alter Baby’s First Microbiome? – Brian Handwerk – Smithsonian

Vaginal Microbes Can Be Partially Restored to C-Section Babies – Heather Buschman – UC San Diego Health

George Weinstock Discusses the Human Microbiome at Eastern – Michael Rouleau – Connecticut State University

‘Holy grail’ bacteria for crop farming debunked by scientists – Hayley Dunning – Imperial College London

Orange slime confirmed to be iron bacteria: Crenothrix polyspora – Herald Net

Iranian Researchers: Extraction of gold, copper from e-waste by two types of bacteria – The Iran Project

Microbes in an ancient mummy : We spoke to study author and microbiologist Dr Frank Maixner about the significance of this new research – MicrobePost
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February 1, 2016

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Vaginal microbiota transplant, temporal sampling of lung microbiota, skin microbiota of a cute frog, extreme CO2 exposure in soil, and microbial mats.

General human microbiome

Human Microbiota of the Argentine Population- A Pilot Study – Belén Carbonetto – Frontiers in Microbiology

Now officially published: Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans – Ron Sender – Cell

Pregnancy and birth

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer – Maria G Dominguez-Bello – Nature Medicine

Chiba study of Mother and Children’s Health (C-MACH): cohort study with omics analyses – Kenichi Sakurai – BMJ Open

Human respiratory microbiome

Prevalence and antimicrobial susceptibility profiles of Staphylococcus aureus nasal carriage among pre-clinical and clinical medical students in a Tanzanian University
Benard Okamo – BMC Research Notes

A case report demonstrating the utility of next generation sequencing in analyzing serial samples from the lung following an infection with influenza A (H7N9) virus –
Yongfeng Hu – Journal of Clinical Virology

Human gut microbiome

Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis – Dmitry A. Ravcheev – Frontiers in Microbiology

Animal models of microbiome research

Research Highlight: Transgenerational missing taxa – Naomi Attar – Nature Reviews Microbiology

Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves – Richard Van Vleck Pereira – PLOS ONE

Animal microbiome

Molecular evidence of vector-borne pathogens in dogs and cats and their ectoparasites in Algiers, Algeria – Amina Bessas – Comparative Immunology, Microbiology and Infectious Diseases

Manatees: Antifungal Resistance and Virulence Among Candida spp. from Captive Amazonian manatees and West Indian Manatees: Potential Impacts on Animal and Environmental Health – José Júlio Costa Sidrim – EcoHealth

Very cute frog: Assessing Antibacterial Potential of Components of Phyllomedusa distincta Skin and its Associated Dermal Microbiota – Ananda Brito de Assis – Journal of Chemical Ecology

Plant, root, and soil microbiome

Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure – Felix Beulig – Nature Microbiology

Precipitation regime drives warming responses of microbial biomass and activity in temperate steppe soils – Weixing Liu- Biology and Fertility of Soils

The diversity of iron reducing bacteria communities in subtropical paddy soils of China – Qi-an Peng – Applied Soil Ecology

Water and extremophile microbiome

Editorial: Systems biology and ecology of microbial mat communities – Martin G. Klotz – Frontiers in Microbiology

Bioreactor microbiology

Microbial communities from 20 different hydrogen-producing reactors studied by 454 pyrosequencing – Claudia Etchebehere – Applied Microbiology and Biotechnology

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions – Man Jae Kwon – PLOS ONE

Performance and microbial community variations in thermophilic anaerobic digesters treating OTC medicated cow manure under different operational conditions – Çağrı Akyol – Bioresource Technology

More microbiology

Acanthamoeba and mimivirus interactions: the role of amoebal encystment and the expansion of the ‘Cheshire Cat’ theory – Ludmila Karen dos Santos Silva – Current Opinion in Microbiology

Gene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome – Rohan Maddamsetti – Mobile Genetic Elements

Microbes in the news

The Bacterium Disappearing From Our Stomachs – H. pylori is losing its foothold – Chau Tu – Science Friday

The Mycobiome: The largely overlooked resident fungal community plays a critical role in human health and disease – Mahmoud Ghannoum – The Scientist

Opportunities for Nanoscience and Nanotechnology in Studying Microbiomes – Paul S Weiss – ACS Nano

“Seeding” The Newborn’s Microbiome – Can We Do It? Should We Be Doing It? – Anne M. Estes – Science & Sensibility

Icy Worlds and their Analog Sites.Fieldwork on Earth provides insight into life’s potential on icy bodies – Keith Cooper – NASA Astrobiology

Bilingual Exhibition Explores the Human Microbiome – Alexandra Mendoza – La Prensa San Diego

Stalin May Have Studied Mao’s Poop in a Secret Lab – Erin Blakemore – Smithsonian

Mapping the Mouth Microbiome – GenEngNews

CosmosID raises $6M to advance microbiome bioinformatics offering – Nick Paul Taylor – Fierce BiotechIt

Science, publishing, and career

The Scientific 23 with Ed Yong: “Science takes us… to the entire natural world, to space, to molecules – things related to humans but not about us.”

How quality control could save your science. It may not be sexy, but quality assurance is becoming a crucial part of lab life – Monya Baker – Nature
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January 27, 2016 – second edition

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A call from the White House, synergy between Mycoplasma and Gardnerella, urinary microbiome, sarcoidosis, and a hiking guide to microbes on the seafloor.

Events

The White House wants feedback from “All Microbiome-Science Champions” – give it – give it now – Jonathan Eisen – MicroBEnet
and
Calling All Microbiome-Science Champions! – Jo Handelsman and Elizabeth Stulberg – The White House

General human microbiome

Review: Exploring and Understanding the Biochemical Diversity of the Human Microbiota – Nitzan Koppel – Cell Chemical Biology

Pregnancy and birth

The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content – Zachery T. Lewis – PeerJ

The common vaginal commensal bacterium Ureaplasma parvum is associated with chorioamnionitis in extreme preterm labour – Ciara Cox – The Journal of Maternal-Fetal & Neonatal Medicine

Human vaginal microbiome

Mycoplasma hominis and Gardnerella vaginalis display a significant synergistic relationship in bacterial vaginosis – C. Cox – European Journal of Clinical Microbiology & Infectious Diseases
Human oral microbiome

The yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodology – Mohsen Sohrabi – Journal of Microbiological Methods

Human skin microbiome

Note: 1 person per study group: Skin microbiota of first cousins affected by psoriasis and atopic dermatitis – Lorenzo Drago – Clinical and Molecular Allergy

Human urinary tract microbiome

Review: The human urinary microbiome and how it relates to urogynecology – Jenifer Schneeweiss – International Urogynecology Journal

Human gut microbiome

Metabolomics connects aberrant bioenergetic, transmethylation, and gut microbiota in sarcoidosis – Andreea Geamanu – Metabolomics

Review: Role of antibiotics for treatment of inflammatory bowel disease – Orna Nitzan – World Journal of Gastroenterology

Review: Gut microbiota imbalance and colorectal cancer – Johan Gagnière – World Journal of Gastroenterology

Animal models

In mice: A detrimental role of immunosuppressive drug, dexamethasone, during Clostridium difficile infection in association with a gastrointestinal microbial shift – Hyeun Bum Kim – Journal of Microbiology and Biotechnology

Animal microbiome

Diversity of the gastric microbiota in Thoroughbred racehorses having gastric ulcer – Hee-Jin Dong – Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest – Ju-pei Shen – Scientific Reports

Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies – Wiebke Sickel – Microbial Ecology

Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia – Yuji Jiang – Soil Biology and Biochemistry

Emergence in mapping microbial diversity in tea (Camellia sinensis (L.) O. Kuntze) soil of Assam, North-East India: A novel approach – PN Bhattacharyya – European Journal of Biotechnology and Bioscience

High-Throughput Sequencing Analysis of the Endophytic Bacterial Diversity and Dynamics in Roots of the Halophyte Salicornia europaea – Shuai Zhao – Current Microbiology

Water and waste microbiome

Use of matrix-assisted laser desorption/ionization–time of flight (MALDI–TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant – Laura Sala-Comorera – International Journal of Hygiene and Environmental Health

Extremophile microbiome

The Guaymas Basin hiking guide to hydrothermal mounds, chimneys and microbial mats: complex seafloor expressions of subsurface hydrothermal circulation – Andreas Teske – Frontiers in Microbiology

Bioinformatics and metagenomics

Bayesian Nonparametric Ordination for the Analysis of Microbial Communities – Boyu Ren – ArXiv

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets – Jai Ram Rideout – PeerJ Preprint

Characterization of sequence-specific errors in various next-generation sequencing systems – Sunguk Shin – Molecular Biosystems

Stochastic neutral modelling of the Gut Microbiota’s relative species abundance from next generation sequencing data – Claudia Sala – BMC Bioinformatics

Protocol: “Deciphering Archaeal Communities” Omics Tools in the Study of Archaeal Communities – Lejla Pašić – Microbial Environmental Genomics (MEG)

Protocol: Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches – Anne Schöler – Microbial Environmental Genomics (MEG)

Science, publishing, and career

Funding: What stops women getting more grants? – David McAllister – Nature

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January 27, 2016

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Catching up after 2 busy days:

Effects of antibiotic use in Finnish children, skin microbiota of salmon transitioning from freshwater to seawater, and California coastal phages.

General human microbiome

Review: The microbial environment and its influence on asthma prevention in early life – Erika von Mutius – Journal of Allergy and Clinical Immunology

Human respiratory tract microbiome

COPD and the microbiome – Manoj J. Mammen – Respirology

Human urinary tract microbiome

Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction – Suzanne L. Groah – The Journal of Urology

Human gut microbiome

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children – Katri Korpela – Nature Communications

Animal models

Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves – Richard Van Vleck Pereira – PLOS ONE

Editorial: Host response: Microbiota prime antiviral response – Julie K. Pfeiffer – Nature Microbiology

Animal microbiome

Comparison of Intestinal Microbiota in Intestinal Tracts of the Wild and Cultured Seahorses, Hippocampus trimaculatus (Leach) – Kai Wang – Journal of the World Aquaculture Society

Social wasps are a Saccharomyces mating nest – Irene Stefanini – PNAS

Transition from freshwater to seawater reshapes the skin-associated microbiota of Atlantic salmon – Jep Lokesh – Scientific Reports

The role of tissue-specific microbiota in initial establishment success of Pacific oysters – Ana Lokmer – Environmental Microbiology

Plant, soil, and root microbiome

Kisameet Clay Exhibits Potent Antibacterial Activity against the ESKAPE Pathogens – mBio

Plant-microbe communication enhances auxin biosynthesis by a root-associated bacterium Bacillus amyloliquefaciens SQR9 – Yunpeng Liu – Molecular Plant-Microbe Interactions

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces – Minsu Kim – PLOS ONE

Analysis of bacterial communities associated with potting media – A. M. Al‑Sadi – Springer Plus

Water microbiome

Persistence of F-Specific RNA Coliphages in Surface Waters from a Produce Production Region along the Central Coast of California – Subbarao V. Ravva – PLOS ONE

Built environment and waste microbiome

Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors – Igor Shuryak – PLOS ONE

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology – Łukasz Jałowiecki – PLOS ONE

Microbial Ecology

The Effect of Immigration on the Adaptation of Microbial Communities to Warming – Diane Lawrence – The American Naturalist

Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process – Sabine Koch – Biotechnology for Biofuels

Microbes in the news

Early-Life Antibiotic Use Affects Gut Microbiome Composition, New Study Says – Genome Web

Classroom research project: detecting phages – MT Standard

 

Uncovering hidden microbial lineages from hot springs – EurekAlert

Your Food’s Bacteria is a Big Data Gold Mine. IBM and Mars are tracking food’s microbiome to improve safety and productivity – David Z. Morris – Fortune

What Causes Cavities? The Balance Of Bacteria In Your Mouth Can Lead To Tooth Decay – Samantha Olson – Medical Daily

First Nations’ ancient medicinal clay shows promise against today’s worst bacterial infections – University of British Columbia

Ferring, Karolinska Institutet Launch Human Microbiome Collaboration – GenEngNews

WTF?: Fat Summit conference: Deepak Chopra Says Bacteria Listen To Our Thoughts – “we are the awakening of bacterial consciousness” – Kavin Senapathy – Forbes
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January 25, 2016

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Today’s digest features biogeography of the human mouth, MALDI-TOF-MS, and microbes from ancient halite. OK, it is technically already Tuesday, but I was busy life tweeting from the Microbiome Symposium today at Stanford. The symposium featured many of the microbiome stars of our University – see my combined life tweets during the conference at Storify

Events

Gut microbiota in health and disease – from concept to evidence – March 17, 2016, Stockholm, Sweden. The symposium will be webcasted live at kva.se and will later be available as video-on-demand at kvatv.se.

Human oral microbiome

Biogeography of a human oral microbiome at the micron scale – Jessica L. Mark Welch – PNAS

Animal models of microbiome research

Experimental modulation of external microbiome affects nestmate recognition in harvester ants (Pogonomyrmex barbatus) – Andy Dosmann – PeerJ

Review: Incorporating the gut microbiota into models of human and non-human primate ecology and evolution – Katherine R. Amato – American Journal of Physical Anthropology

Animal microbiome

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

Extremophile microbiome

Review: Buried Alive: Microbes from Ancient Halite – Salla T. Jaakkola – Trends in Microbiology

Food microbiology

Effect of X-ray treatments on Escherichia coli O157:H7, Listeria monocytogenes, Shigella flexneri, Salmonella enterica and inherent microbiota on whole mangoes – B.S.M. Mahmoud – Letters in Applied Microbiology

Techniques

Advantage of MALDI-TOF-MS over biochemical-based phenotyping for microbial identification illustrated on industrial applications – S.K. Urwyler – Letters in Applied Microbiology

More microbiology

Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training – André Antunes – Trends in Microbiology

Microbes in the news

Do probiotics cure asthma? Don’t believe the hype: Jonathan Eisen awards “prizes” to those who “oversell the microbiome” – Emma Bryce – Wired

The Forest In Your Mouth – Ed Yong – Phenomena National Geographic

Take your kids to the bugs on a Sunday afternoon – Micropia, the world’s only microbe zoo in Amsterdam – Mathias Grote – ASM Blog

IS-diagnostics Publishes Validation of PCR-Based Clinical Metagenomic MDx –  Madeleine Johnson – Genome Web

Bacteria Hysteria

Bacteria won’t wash, with the Brushield toothbrush cover – GizMag

Science, publishing, and career

#ResearchParasites and #ScienceColonialism – featuring Tweets from @DNLee5 & some discussion – Jonathan Eisen – Storify

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January 23, 2016

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Maturation of the mucin layer, periodontitis in Sjögren’s, Caenorhabditis elegans gut microbiota assembly, the rice-osphere, archaea in moonmilk, and microbial arsenic metabolism.

General human microbiome

The Human Microbiome and Public Health: Social and Ethical Considerations – Kieran C. O’Doherty – American Journal of Public Health

Pregnancy and birth

Review: Mucin–Microbiota Interaction During Postnatal Maturation of the Intestinal Ecosystem: Clinical Implications – Sana Rokhsefat- Digestive Diseases and Sciences

Human oral microbiome

Periodontitis prevalence and serum antibody reactivity to periodontal bacteria in primary Sjögren’s syndrome: a pilot study – Bozo Lugonja – Journal of Periodontology

Temporal Stability of the Salivary Microbiota in Oral Health – Daniel Belstrøm – PLOS ONE

Review: Immune dysregulation mediated by the oral microbiome: potential link to chronic inflammation and atherosclerosis – C. Slocum – Journal of Internal Medicine

Human gut microbiome

Review: Microbiota manipulation for weight change – Tal Dror – Microbial Pathogenesis

Review: Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances – M. P. Francino – Frontiers in Microbiology

Models of microbiome research

Modulating the Gut Microbiota Improves Glucose Tolerance, Lipoprotein Profile and Atherosclerotic Plaque Development in ApoE-Deficient Mice – Ida Rune – PLOS ONE

Dysbiosis of the fecal microbiota in the TNBS-induced Crohn’s disease mouse model – Qing He – Applied Microbiology and Biotechnology

Animal microbiome

Note that the worms did not develop into adults without having veggies to eat: Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments – Maureen Berg – The ISME Journal

Plant, root, and soil microbiome

Rice-osphere? Rice Genotype Differences in Tolerance of Zinc-Deficient Soils: Evidence for the Importance of Root-Induced Changes in the Rhizosphere – Asako Mori – Frontiers in Plant Science

A perspective on inter-kingdom signaling in plant–beneficial microbe interactions – Amanda Rosier – Plant Molecular Biology

Chemotaxis signaling systems in model beneficial plant–bacteria associations – Birgit E. Scharf – Plant Molecular Biology

Water and extremophile microbiome

Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system – Helena Osterholz – The ISME Journal

Unique pioneer microbial communities exposed to volcanic sulfur dioxide – Reiko Fujimura – Scientific Reports

Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential – Christoph Reitschuler – Microbial Ecology

Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria – Steven Smriga – PNAS

Review: The microbial genomics of arsenic – Jérémy Andres – FEMS Microbiology Reviews

Food microbiology

Kombucha tea fermentation: Microbial and biochemical dynamics – Somnath Chakravorty – International Journal of Food Microbiology

PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment – Obinna T. Ezeokoli – International Journal of Food Microbiology

Check your fridge for Thanksgiving leftovers: Direct Dynamic Kinetic Analysis and Computer Simulation of Growth of Clostridium perfringens in Cooked Turkey during Cooling – Lihan Huang – Journal of Food Science

Bioinformatics, metagenomics, and protocols

Protocol collection: Microbial Environmental Genomics (MEG)
MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function – Kevin P. Keegan
Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches – Anne Schöler
Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip – Joy D. Van Nostrand
Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning – Céline Ribière
Fungal Communities in Soils: Soil Organic Matter Degradation – Tomáš Větrovský
GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity – Samuel Dequiedt

Microbes in the news

Exploring the human gut microbiome. Scientific interest in this diverse world of bacteria has flipped from fear to fascination – Sabin Russell – Fred Hutch

Fungi Prevalent in Urine of Women With Chronic Pelvic Pain – Pam Harrison – MedPageToday

Microscopic subway passengers with a ticket to ride: Interview with Chris Mason – Labnews

To Fight Growing Threat From Germs, Scientists Try Old-Fashioned Killer – Gautam Naik – The Wall Street Journal

http://www.cnn.com/2016/01/22/health/flint-water-legionnaires-disease/Flint hospital reports finding Legionnaires’ bacteria in water – Ralph Ellis – CNN

Breast milk protein could be used in fight against antibiotic resistance – The Guardian

Listeria outbreak: Dole packaged salad linked to 12 bacteria infections and one death – John Houck – Inquisitr

Science, publishing, and career

By a 13 year old girl: Letter to BBC Wildlife Magazine on sexism in nature conservation – Mya-Rose Craig – BirdGirl

Bik’s Picks

Secular trends in family dinner frequency among adolescents – Kathryn Walton – BMC Research Notes
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January 22, 2016

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Viruses in desert soils, pneumonia etiology, and a concerning editorial in NEJM.

Human oral microbiome

Microbiological analysis after complete or partial removal of carious dentin using two different techniques in primary teeth: A randomized clinical trial – Deepak Kumar Singhal – Dental Research Journal

Human respiratory microbiome

The Modern Quest for the “Holy Grail” of Pneumonia Etiology – Seema Jain – Clinical Infectious Diseases

Plant, root, and soil microbiome

Review: Diversity and Ecology of Viruses in Hyperarid Desert Soils – Olivier Zablocki – Applied and Environmental Microbiology

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil – Matthew J. Meier – Applied and Environmental Microbiology

Techniques / phages and viruses

Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches – Pingfeng Yu – Applied and Environmental Microbiology

More microbiology

Tuberculosis in Newborns: The Lessons of the “Lübeck Disaster” (1929–1933) – Gregory J. Fox – PLOS Pathogens

Microbes in the news

For children: Understanding Marine Microbes, the Driving Engines of the Ocean – Anna Kopf

15 min podcast: A Microbiome Is Born – Science Friday

Good Bacteria for Good Skin – Beauty brands say there is a beneficial effect when probiotics and fermented ingredients are applied topically – Fiorella Valdesolo – Wall Street Journal

Your DNA could make you resistant to certain bacteria – gene expression could help explain why some people are more immune to infection than others – Alexandra Ossola – Popular Science

Science, publishing, and career

An editorial in NEJM called Data Sharing, written by Dan L. Longo and Jeffrey M. Drazen, caused a lot of concern because it calls scientists who use other people’s published data “parasites”. Some reactions:

Data Scientists = Research Parasites? – David Shaywitz – Forbes

Research “parasitism” and authorship rights – Leonid Schneider – For Better Science

Attack of the Research Parasites – Derek Lowe – Science Magazine blogs

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