Category Archives: Microbial Ecology

February 20, 2016

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Effects of ocean acidification, structural proteins in viral dark matter, and microbiome art. Also check out my new post at MicroBE.net with new papers on microbiome of the built environment.

Human respiratory tract microbiome

Review: How Recent Advances in Molecular Tests Could Impact the Diagnosis of Pneumonia – David Murdoch – Expert Review of Molecular Diagnostics

Microbiome models

In vitro fermentation of alginate and its derivatives by human gut microbiota – Miaomiao Li – Anaerobe

Plant, root, and soil microbiome

Changes of soil prokaryotic communities after clear cutting in a karst forest: evidences for cutting-based disturbance promoting deterministic processes – Xiao Zhang – FEMS Microbiology Ecology

Use of mulberry–soybean intercropping in salt–alkali soil impacts the diversity of the soil bacterial community – Xin Li – Microbial Biotechnology

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments – Lidianne L. Rocha – International Journal of Microbiology

Water and ice microbiome

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches – Christiane Hassenrück – FEMS Microbiology Ecology

Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice – Ido Hatam – The ISME Journal

Bioreactor and waste microbiology

Biodegradation of different petroleum hydrocarbons by free and immobilized microbial consortia – Tiantian Shen – Environmental Science: Processes & Impacts

Bioinformatics and metagenomics

Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms – Ayyappa kumar Sista Kameshwar – International Journal of Biological Sciences

DUDE-Seq: Fast, flexible, and robust denoising of nucleotide sequences – Byunghan Lee – Bioinformatics

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing – Ramin Karimi – Evolutionary Bioinformatics

FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance – Syun-ichi Urayama – Microbes and Environments

Based on my old discovery of the mycobacterial CRISPR: SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads – Eryu Xia – Genome Medicine

Microbial ecology

A tradeoff between the ecological and evolutionary stabilities of public goods genes in microbial populations – Joseph Rauch – BioRxiv

Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations – Tatiana Shashkova – PLOS ONE

Proteomics

Illuminating structural proteins in viral “dark matter” with metaproteomics – Jennifer R. Brum – PNAS

Microbes in the news

‘Unhealthy’ Microbiomes Could Promote Metabolic Disease. UCSF Symposium Explores Vulnerability and Malleability of Microbes in Human Gut – Nicholas Weiler – University of California San Francisco

Unusual sugar in leafy greens may help gut bacteria protect health – Catharine Paddock – Medical News Today

One startup’s plan to grow more crops: put the germs back in. Indigo claims it can dramatically boost yields by restoring plant’s microbiome – Ben Popper – The Verge

The intestinal microbiota—a new ally for optimum growth – Medical Xpress

Bacteria In Contact Lenses May Cause Inflammatory Response Leading To Microbial Keratitis / Gross Science Video with Anna Rothschild – Lizette Borreli – Medical Daily

Bacteria Hysteria

Tea crawling with harmful bacteria and food trays covered in faeces: The horror health threats facing airline passengers – The Sun

Microbes and art

Faces of BioArt: Sonja Bäumel’s Microbiome Portraits and Bacterial Clothing – Labiotech

Science, publishing, and career

Put the “Ph” Back in PhD. We need big thinkers, but the current system teaches students to think small – Arturo Casadevall

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February 19, 2016

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My PhD anniversary today! Today I found papers on primary sclerosing cholangitis, fungi from goat guts, dispersal from biofilms.

Human gut microbiome

The gut microbial profile in patients with primary sclerosing cholangitis is distinct from patients with ulcerative colitis without biliary disease and healthy controls – Martin Kummen – Gut

Review: Obesity, Asthma, and the Microbiome – Youngji Cho – Physiology

Microbiology of infection

Bacterial biofilm infection detected in breast implant associated anaplastic large cell lymphoma – Hu, Honghua – Plastic and Reconstructive Surgery

Animal models

Peripheral Lymphoid Volume Expansion and Maintenance Are Controlled by Gut Microbiota via RALDH+ Dendritic Cells – Zongde Zhang – Immunity

Important Metabolic Pathways and Biological Processes Expressed by Chicken Cecal Microbiota – Ondrej Polansky – Applied and Environmental Microbiology

Lingonberries reduce atherosclerosis in Apoe-/- mice in association with altered gut microbiota composition and improved lipid profile – Chrysoula Matziouridou – Molecular Nutrition & Food Research

Emerging role of lipid droplets in Aedes aegypti immune response against bacteria and Dengue virus – Ana Beatriz Ferreira Barletta – Scientific Reports

Animal microbiome

Goats! Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes – Kevin V. Solomon – Science

Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii – Hyatt C. Green – Applied and Environmental Microbiology

Mucosal immunoglobulins at respiratory surfaces mark an ancient association that predates the emergence of tetrapods – Zhen Xu – Nature Communications

Plant, root, and soil microbiome

Opposing phylogenetic diversity gradients of plant and soil bacterial communities – Marta Goberna – Proceedings of the Royal Society B

Water microbiome

Functional metagenomic screen reveals new and diverse microbial rhodopsins – Alina Pushkarev – The ISME Journal

Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen Genes in Riverine and Marine Systems – Xiang Li – Applied and Environmental Microbiology

Pathogens in Ornamental Waters: A Pilot Study – Maria Nascimento – MDPI Int. J. Environ. Res. Public Health

More Microbiology

What Makes a Bacterial Species Pathogenic? Comparative Genomic Analysis of the Genus Leptospira – Derrick E. Fouts – PLOS NTD

Go Forth and Colonize: Dispersal from Clinically Important Microbial Biofilms – Priya Uppuluri – PLOS Pathogens

Microbes in the news

Fungi from goats’ guts could lead to better biofuels – Matt McGrath – BBC News

Mapping the microbes in your mouth: We spoke to lead author Dr Gary Borisy about the research published in PNAS this month. – Microbe Post

Penn Study Reveals How Fish Control Microbes Through Their Gills – PennNews

93% of Israel’s Fresh Chicken Has Dangerous Bacteria (Campylobacter) – Forward

Electroporation 2.0: Breaking through the bacteria barrier: New microfluidic device may speed up DNA insertion in bacteria, the first step in genetic engineering – MIT News

Gut Microbes and Milk Compounds Tackle Childhood Malnutrition – Pat Bailey – UC Davis

Porcine Probiotic May Help Protect Gut Health – Susan Bubak – University of Guelph
Could Fecal Transplants From Rich Children Help Starving Kids in Africa? – Kari Paul – Motherboard

BiofilmDNA oral microbial salivary test to be launched by Oravital Inc. during 2016 Chicago Midwinter Meeting – DentistryIQ

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February 18, 2016

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Two papers from the Gordon lab today about malnutrition and gut microbes, connecting gut microbes with host chitin, fur seals, and analyzing soil communities for forensic use.

Pregnancy and birth

(partly in mice) Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children – Laura V. Blanton – Science

Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition – Mark R. Charbonneau – Cell

Editorial: The right gut microbes help infants grow – Elizabeth Pennisi – Science

Stool bacterial load in preterm infants with necrotising enterocolitis – Bashir Abdulkadir – Early Human Development

Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study – Guilherme Calvet – The Lancet Infectious Diseases

Human gut microbiome

Gut Microbiota Predict Pulmonary Infiltrates After Allogeneic Hematopoietic Cell Transplantation – Bianca Harris – Am J Respir Crit Care Med

Members of the Intestinal Microbiota Are Associated with Relapse after Allogeneic Hematopoietic Stem Cell Transplantation – Jonathan U. Peled – Biology of Blood and Marrow Transplantation

Conference abstract: Fecal Microbiota Transplant Is a Potentially Safe and Effective Treatment for Clostridium Difficile Infection in Hematopoietic Stem Cell Recipients – Shannon Falconer – Biology of Blood and Marrow Transplantation

The impact of gut colonization by antibiotic-resistant bacteria on the outcomes of allogeneic hematopoietic stem-cell transplantation: a retrospective, single-center study – Jaroslaw Bilinski – Biology of Blood and Marrow Transplantation

 

PhD Thesis: Temporal Modulation of Gut Microbiome and Metabolome by Morphine – Fuyuan Wang – University of Minnesota

Research highlight: Frailty associated with gut microbiota – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Review: Exploring the Microbiome in Heart Failure – Takeshi Kitai – Current Heart Failure Reports

Perspective: The microbiome and development of allergic disease – Susan V. Lynch – Current Opinion in Allergy and Clinical Immunology

Hypothesis: The gut microbiota: A puppet master in the pathogenesis of endometriosis? – Matthias W. Laschke – American Journal of Obstetrics and Gynecology

Editorial: Microbiota, Obesity and Malnutrition – Didier Raoult – Microbial Pathogenesis

Review: Protective and Pro-Inflammatory Roles of Intestinal Bacteria – Cynthia Reinoso Webb – Pathophysiology

Models of microbiome

Mice: Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals – Alexandra Montagner – Scientific Reports

Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition – Martin Schwarzer – Science

Mice: Butyrate production from high-fiber diet protects against lymphoma tumor – Wei Wei – Leukemia & Lymphoma

Drosophila: Sex difference in pathology of the ageing gut mediates the greater response of female lifespan to dietary restriction – Jennifer C Regan – eLIFE

Mice: Treatment with a Monoclonal Anti-IL-12p40 Antibody Induces Substantial Gut Microbiota Changes in an Experimental Colitis Model – Josué Castro-Mejía – Gastroenterology Research and Practice

Mice: Diets enriched with cranberry beans alter the microbiota and mitigate colitis severity and associated inflammation – Jennifer M. Monk – The Journal of Nutritional Biochemistry

Research Highlight: Microbiota promote gut healing – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Gut immunity in a protochordate involves a secreted immunoglobulin-type mediator binding host chitin and bacteria – Larry J. Dishaw – Nature Communications

Characterisation of the faecal bacterial community of wild young South American (Arctocephalus australis) and Subantarctic fur seals (Arctocephalus tropicalis) – Aline Weber Medeiros – FEMS Microbiology Ecology

16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife: the importance of cleaning post-sequencing data before estimating positivity, prevalence and co-infection – Maxime Galan – bioRxiv

Nestedness of hoopoes’ bacterial communities: symbionts from the uropygial gland to the eggshell – Juan J. Soler – Biological Journal of the Linnean Society

Plant, root, and soil microbiome

Biogeographic Patterns Between Bacterial Phyllosphere Communities of the Southern Magnolia (Magnolia grandiflora) in a Small Forest – Bram W. G. Stone – Microbial Ecology

Culturable endophytic bacteria from the salt marsh plant Halimione portulacoides: phylogenetic diversity, functional characterization, and influence of metal(loid) contamination – Cátia Fidalgo – Environmental Science and Pollution Research

Next-Generation Sequencing of the Bacterial 16S rRNA Gene for Forensic Soil Comparison: A Feasibility Study – Ellen M. Jesmok – Journal of Forensic Sciences

Water microbiome

Sediments and Soils Act as Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River – Christopher Staley – Microbial Ecology

The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem – Adam S. Wymore – Microbial Ecology

Built environment microbiome

Commentary: Making microbiology of the built environment relevant to design – G. Z. Brown – Microbiome

Food microbiology

Changes of microbial spoilage, lipid-protein oxidation and physicochemical properties during post mortem refrigerated storage of goat meat – Azad Behnan Sabow – Animal Science Journal

Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota – Alejandra Escobar-Zepeda – Food Microbiology

Bioinformatics

An analysis of human microbe–disease associations – Wei Ma – Briefings in Bioinformatics

FN-Identify: Novel Restriction Enzymes-Based Method for Bacterial Identification in Absence of Genome Sequencing – Mohamed Awad – Advances in Bioinformatics

Microbial ecology

Capturing the Dynamic, Heterogeneous Response of Microbes to their Environment in the Human Microbiome – Julie Biteen – Biophysical Journal

Perspective: Microbial community modeling using reliability theory – Julie L Zilles – The ISME Journal

Microbes in the news

Could the right gut microbes help fight childhood malnutrition? – Rachel Feltman – Washington Post

Breast Milk Sugars Support Infant Gut Health – Anna Azvolinsky – The Scientist

Targeting gut microbes may reverse effects of childhood malnutrition
Healthy microbes, breast milk component suggest new treatment approach, mouse study shows – Julie Evangelou Strait – Washington University

How Microbes Make Malnutrition Worse. And how they can be marshaled to fight it – Ed Yong – The Atlantic

 

The Mushroom Death Suit is the latest in post-mortem, eco-friendly fashion – Atlas Obscura

Through Metagenomics Analysis, Researchers Uncover Zika Virus Genome in Amniotic Fluid – Genome Web

What’s bugging you now? The amazing potential of our bodies’ own bacteria – Trisha Macnair – Spectator Health

Gut bacteria may be the difference between well-fed and malnourished – Jacob Kastrenakes – The Verge

Creative Minds: Bacteria, Gene Swaps, and Human Cancer, featuring Julie Dunning Hotopp – Francis Collins – NIH Director’s Blog

This Startup Wants to Use Bacteria to Revolutionize How Our Food Is Produced – Beth Kowitt – Fortune

Bacteria Hysteria

Dad warns parents about Sistema Twist ‘N’ Sip drink bottles ‘hoarding bacteria’ – Stuff

Breast Milk Bought Online May Contain Bacteria That Could Harm Your Child, Investigation Finds – Inside Edition

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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 24, 2016

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Antibiotic therapy in preterm labor, shrimp microbial dynamics, volcanic desert on Mount Fuji, coffee processing, and Antarctic permafrost limits microbial life.

Pregnancy and birth

Antibiotic Therapy Increases the Risk of Preterm Birth in Preterm Labor without Intra-Amniotic Microbes, but may Prolong the Gestation Period in Preterm Labor with Microbes, Evaluated by Rapid and High-Sensitive PCR System – Satoshi Yoneda – American Journal of Reproductive Immunology

Human gut microbiome

Does the Intestinal Microbiota Explain Differences in the Epidemiology of Liver Disease between East and West – Nakamoto N. – Inflammatory Intestinal Diseases

Commentary: Microbiome-based companion diagnostics: no longer science fiction?
Jeroen Raes – Gut

Animal microbiome

Diary of a shrimpy kid: Dynamic changes of microbial communities in Litopenaeus vannamei cultures and the effects of environmental factors – Hao Zhang – Aquaculture

Plant, root, and soil microbiome
Substrate limitation to soil microbial communities in a subalpine volcanic desert on Mount Fuji, Japan – S. Yoshitake – European Journal of Soil Biology

Bottom-up control of fertilization on soil nematode communities differs between crop management regimes – Ting Liu – Soil Biology and Biochemistry

Interactive effects of precipitation and nitrogen spatial pattern on carbon use and functional diversity in soil microbial communities – Nianxun Xi – Applied Soil Ecology

Water and extremophile microbiome

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica – Jacqueline Goordial – The ISME Journal

Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments – Petter Thureborn – PeerJ

 

Waste treatment microbiology

Metagenomic and quantitative insights into microbial communities and functional genes of nitrogen and iron cycling in twelve wastewater treatment systems – Duntao Shu – Chemical Engineering Journal

Food microbiology

High throughput sequencing identifies novel viruses in nectarine: Insights to the etiology of stem pitting disease – Dan Edward Veloso Villamor – Phytopathology

DGGE: Discrimination of post-harvest coffee processing methods by microbial ecology analyses – Yasmine Hamdouche – Food Control

Microbial Ecology

Integrating Theory and Experiment to Explain the Breakdown of Population Synchrony in a Complex Microbial Community – Emma J. Bowen – arXiv

Techniques

Poster abstract: Assembling Whole Genomes from Mixed Microbial Communities Using Hi-C – Ivan Liachko – Plant and Animal Genome Conference

Microbes in the news

Antarctic permafrost may not be habitable for microbes – so is Mars? Finding life on Mars might be harder than thought — or Martian microbes might be different – Emily Chung – CBC News

Microbes take their vitamins — for the good of science – EurekAlert

Bacteria that resist last-resort antibiotics were found in China two months ago, now they’re everywhere – Dominic Jackson – Shanghaiist

Newly Discovered Photosynthetic Bacteria Is Surprisingly Abundant – Science 2.0

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January 16, 2016

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Gut microbiota in acute malnutrition, social behavior and the chimpanzee pan-microbiome, arctic marine fungi, and learning ecological networks.

General microbiome

Immune-Microbiota Interactions: Dysbiosis as a Global Health Issue – Alan C. Logan – Current Allergy and Asthma Reports

Human oral microbiome

Long-term prospective cohort study on dental implants: clinical and microbiological parameters – Henri Tenenbaum – Clinical Oral Implants Research

Human reproductive tract microbiome

Alterations in the Genital Microbiota in Women With Spinal Cord Injury – Pires, Cristhiane V.G. – Obstetrics & Gynecology

Human gut microbiome

Gut Microbiota in Children Hospitalized with Oedematous and Non-Oedematous Severe Acute Malnutrition in Uganda – Kia Hee Schultz Kristensen – PLOS Neglected Tropical Diseases

Editorial: Confounding Effects of Metformin on the Human Gut Microbiome in Type 2 Diabetes – Adil Mardinoglu – Cell Metabolism

Review: Impact of high fat diets, prebiotics and probiotics on gut microbiota and immune function, with relevance to elderly populations – Yue Liu – Nutrition and Aging

Review: Transkingdom control of viral infection and immunity in the mammalian intestine – Julie K. Pfeiffer – Science

Review: Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality – Rosemarie De Weirdt – NPJ Biofilms and Microbiomes

Animal models

In rats: Alternating or continuous exposure to cafeteria diet leads to similar shifts in gut microbiota compared to chow diet – Nadeem O. Kaakoush – Molecular Nutrition & Food Research

In mice: Streptomycin treatment alters the intestinal microbiome, pulmonary T cell profile and airway hyperresponsiveness in a cystic fibrosis mouse model – Mark Bazett – Scientific Reports

Animal microbiome

Social behavior shapes the chimpanzee pan-microbiome – Andrew H. Moeller – Science Advances

Environmental drivers of microbial community shifts in the giant barrel sponge, Xestospongia muta, over a shallow to mesophotic depth gradient – Kathleen M. Morrow – Environmental Microbiology

Feeding cessation alters host morphology and bacterial communities in the ascidian Pseudodistoma crucigaster – Susanna López-Legentil – Frontiers in Zoology

Plant, root, and soil microbiome

Uncultivated margins are source of soil microbial diversity in an agricultural landscape –
Luciana D’Acunto – Agriculture, Ecosystems & Environment

Editorial: Deep influence of soil microbes – Karl Gruber – Nature Plants

Review: Soil microbes and community coalescence – Matthias C. Rillig – Pedobiologia

Water and extremophile microbiome

Linkages between mineralogy, fluid chemistry, and microbial communities within hydrothermal chimneys from the Endeavor Segment, Juan de Fuca Ridge – T. J. Lin – Geochemistry, Geophysiscs, Geosystems

Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater lake within basalt rock – Dhiraj Paul – Frontiers in Microbiology

Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond – Shimin Lu – Frontiers in Microbiology

Chytrids Dominate Arctic Marine Fungal Communities – B.T. Hassett – Environmental Microbiology

Built environment microbiome

Bacterial Monitoring in the International Space Station-“Kibo” Based on rRNA Gene Sequence – Nobuyasu Yamaguchi – Transactions of the Japan Society for Aeronautical and Space Sciences

Metagenomics and bioinformatics

Safe and complete contig assembly via omnitigs – Alexandru I. Tomescu – ArXiv

More microbiology and ecology

How clonal are bacteria over time? – B. Jesse Shapiro – BioRxiv

Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes – Edgardo Galán-Vásquez – PLOS ONE

Learning Ecological Networks from Next-Generation Sequencing Data – Corinne Vacher – Advances in Ecological Research

Microbes in the news

Chimps Share Microbes When Socializing – Kate Yandell – The Scientist

How Your Social Life Changes Your Microbiome – Ed Yong – The Atlantic

Social Contact Helps Beneficial Gut Bacteria Spread – Brian Handwerk – Smithsonian

Prevent severe diarrhea by controlling levels of specific gut bacteria – Bel Marra Health

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December 31, 2015

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Last post of the year! Wishing you and all microbiomes a great, successful and healthy 2016!

Dead or alive in the sinus microbiome, early life exercise, feather degrading bacteria in the house sparrow, and fungi on public restroom floors.

Pregnancy and birth

Review: The Influence of Early Infant-Feeding Practices on the Intestinal Microbiome and Body Composition in Infants – Aifric O’Sullivan – Nutrition and Metabolic Insights

Human oral microbiome

Review: Advances in the microbial etiology and pathogenesis of early childhood caries –
Evlambia Hajishengallis – Molecular Oral Microbiology

Human respiratory tract microbiome

Dead or alive: Deoxyribonuclease I sensitive bacteria and implications for the sinus microbiome – A.L. Williams – American Journal of Rhinology & Allergy

Human gut microbiome

Early life exercise may promote lasting brain and metabolic health through gut bacterial metabolites – Agnieszka Mika – Immunology & Cell Biology

Proton pump inhibitors alter the composition of the gut microbiota – Matthew A Jackson – Gut

Metagenomic Analysis Reveals Dynamic Changes of Whole Gut Microbiota in the Acute Phase of Intensive Care Unit Patients – Masahiro Ojima – Digestive Diseases and Sciences

Review: Dietary Emulsifiers, The Human Intestinal Mucus and Microbiome, and Dietary Fiber – Michael J. Glade – Nutrition

Review: Commensal bacteria modulate the tumor microenvironment – Theofilos Poutahidis – Cancer Letters

Review: Characterizing the Intestinal Microbiome in Infantile Colic. Findings Based on an Integrative Review of the Literature – Nancy E. Dubois – Biological Research For Nursing

Microbiome models

Variability in microbial population and fermentation traits at various sites within the forestomach and along the digestive tract as assessed in goats fed either grass or browse – J.O. Zeitz – Small Ruminant Research

Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis) – Neelam M. Nathani – BMC Genomics

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

Animal microbiome

Birds: Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe – Zoë L. Grange – Microbial Ecology

More birds: Feather-degrading bacteria, uropygial gland size and feather quality in House Sparrows Passer domesticus – Attila Fülöp – Ibis

Plant, root, and soil microbiology

The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria – Marjolaine Martin – Frontiers in Microbiology

Characterization of Arbuscular Mycorrhizal Fungus Communities of Aquilaria crassna and Tectona grandis Roots and Soils in Thailand Plantations – Amornrat Chaiyasen – PLOS ONE

Water and extremophile microbiome

Characterization of Halophilic Bacterial Communities in Turda Salt Mine (Romania) – Rahela Carpa – Origins of Life and Evolution of Biospheres

Built environment microbiome

Rapid assemblage of diverse environmental fungal communities on public restroom floors – Jennifer Fouquier – Indoor Air

A simple novel device for air sampling by electrokinetic capture – Julian Gordon – Microbiome

Infection microbiology

Review: The biogeography of polymicrobial infection – Apollo Stacy – Nature Reviews Microbiology

Microbes in the news

Gut Microbiome Influenced by Early-Life Exercise – GenEngNews

Celebrating the good viruses of 2015 – Jason Tetro – Popular Science

End of the year lists

Science: Best long reads of 2015 (part one) – BBC

Science: Best long reads of 2015 (part two) – BBC

Science, publishing, and career

“Women Who Don’t Give a Crap” – Holly Tabor – PLOS Genetics

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December 30, 2015

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Gut microbiomes of birds, mammals, and ray-finned fishes, metabolic pathways in the chicken cecum, fungi in sand dunes, and bacterioplankton in tilapia ponds.

Human gut microbiome

Role of the gut microbiota of children in diarrhea due to the protozoan parasite Entamoeba histolytica – Carol A. Gilchrist – The Journal of Infectious Diseases

Microbiome models

Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses – Darren Ruane – Journal of Experimental Medicine

Role of the Gut Microbiome in Obstructive Sleep Apnea–Induced Hypertension – David J. Durgan – Hypertension

Animal microbiome

Identification of specialists and abundance-occupancy relationships among intestinal bacteria of Aves, Mammalia, and Actinopterygii – Hyatt C. Green – Applied and Environmental Microbiology

Lactic Acid Bacteria Isolated from Bovine Mammary Microbiota: Potential Allies against Bovine Mastitis – Damien S. Bouchard – PLOS ONE

Characterisation of the most important metabolic pathways and biological processes expressed in chicken caecal microbiota – Ondrej Polansky – Applied and Environmental Microbiology

Bacterial Profiling Reveals Novel “Ca. Neoehrlichia”, Ehrlichia, and Anaplasma Species in Australian Human-Biting Ticks – Alexander W. Gofton – PLOS ONE

Fickle or Faithful: The Roles of Host and Environmental Context in Determining Symbiont Composition in Two Bathymodioline Mussels – Sven R. Laming – PLOS ONE

Plant, root, and soil microbiome

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis – Alice Roy-Bolduc – Ecology and Evolution

The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome – Youry Pii – Plant Physiology and Biochemistry

Water and waste microbiome

Bacterioplankton community analysis in tilapia ponds by Illumina high-throughput sequencing – Li Min Fan – World Journal of Microbiology and Biotechnology

Bioremediation of diesel contamination at an underground storage tank site: a spatial analysis of the microbial community – Marco Andreolli – World Journal of Microbiology and Biotechnology

Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status – Yu Dai – Applied Microbiology and Biotechnology

Microbial Ecology

In silico gene-level evolution explains microbial population diversity through differential gene mobility – Bram van Dijk – Genome Biology and Evolution

Microbes in the news

Genome watch: Viral fossils: increased availability of mammalian genomes provides new insights – Astrid Gall – Nature Reviews Microbiology

Drugs for your bugs: targeting the microbial enzymes involved in TMA metabolism – Cláudio Nunes-Alves – Nature Reviews Microbiology

Q&A: Cocktail maker: Tim Lu’s synthetic-biology research at Massachusetts Institute of Technology – Will Tauxe – Nature
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December 13, 2015

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Apple juice or almond consumption, lessons from animal studies, distinguishing between live and dead methanogens.

Human gut microbiome

Comparative study of fecal microbiota in patients with type II diabetes after consumption of apple juice for 4 weeks – Gyu-Sung Cho – Food Science and Biotechnology

Diet quality improves for parents and children when almonds are incorporated into their daily diet: a randomized, crossover study – Alyssa M. Burns – Nutrition Research

Review: Diagnosis and treatment of small intestinal bacterial overgrowth – Francesca Romana Ponziania – Expert Review of Gastroenterology & Hepatology

Review: The enteric microbiome in hepatobiliary health and disease – James H. Tabibian – Liver International

Animal models

Review: The influence of the young microbiome on inflammatory diseases—Lessons from animal studies – Katja M. Bendtsen – Birth Defects Research Part C: Embryo Today: Reviews

Plant, root, and soil microbiome

Interaction between lithification and resource availability in the microbialites of Río Mesquites, Cuatro Ciénegas, México – J. R. Corman – Geobiology

The diversity and abundance of phytase genes (BPP) in bacterial communities of the maize rhizosphere – Simone Raposo Cotta – Letters in Applied Microbiology

Bring on the wheelbarrow: Transplanting soil microbiomes leads to lasting effects on willow growth, but not on the rhizosphere microbiome – Etienne Yergeau – Frontiers in Microbiology

Differential responses of soil bacterial taxa to long-term P, N, and organic manure application – Ying Wang – Journal of Soils and Sediments

Water and extremophile microbiome

Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California – Luke McKay – Environmental Microbiology Reports

Oceanic fronts: transition zones for bacterioplankton community composition – Federico Baltar – Environmental Microbiology Reports

PhD thesis: Hydrothermal Habitats: Measurements of Bulk Microbial Elemental Composition, and Models of Hydrothermal Influences on the Evolution of Dwarf Planets – Marc Francois Luarent Neveu – Arizona State University

Metagenomics and bioinformatics

Network construction and structure detection with metagenomic count data – Zhenqiu Liu – BioData Mining

A simple algorithm for identifying integrons and gene cassettes in bacteria on next generation sequencing data – Guan-Jie Hua – International Journal of Data Mining and Bioinformatics (no access for me)

Techniques

Fluorescent in situ hybridization for the localization of viruses, bacteria and other microorganisms in insect and plant tissues – Adi Kliot – Methods

Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples – Janine Heise – Journal of Microbiological Methods

Microbes in the news

You’re Surrounded by Bacteria That Are Waiting for You to Die – Erika Engelhaupt – National Geographic

Does That Wine Smell Good? Bacteria in Your Saliva Deserve Some of the Credit
Study shows some wine aromatics aren’t released until they meet the bacteria in our mouths – Kasey Carpenter – Wine Spectator

San Jose: Hospital nurse had tuberculosis; hundreds of babies, moms need treatment or tests – Tracy Seipel – Mercury News

Based on a 2006 paper: This Weed Takes Out Other Plants by Attacking Their “Gut Bacteria” – Esther Inglis-Arkell – Gizmodo

Bacteria Hysteria

Could your child’s teddy give them a stomach bug? Wash youngsters’ favourite toys… and other tips to keep your family lurgy-free this Christmas – The Sun

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December 2, 2015

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General microbiome

Microbiology: Microbiome studies need local leaders – Victor S. Pylro – Nature

Human skin microbiome

Conclusions not strongly supported by data: Chitosan Coated Textiles May Improve Atopic Dermatitis Severity by Modulating Skin Staphylococcal Profile: A Randomized Controlled Trial – Cristina Lopes – PLOS ONE

Human respiratory microbiome

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome – Robert A Quinn – The ISME Journal

Perspective: In the name of ventilator-associated pneumonia prevention: lung microbiota blown away by colistin! – Saad Nseir – European Respiratory Journal

Human gut microbiome

Better link than yesterday: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Kristoffer Forslund – Nature

Animal microbiome

Human Staphylococcus aureus lineages among Zoological Park residents in
Greece – E. Drougka – Open Veterinary Journal

Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions – Xiaoling Wan – Current Microbiology

Plant, root, and soil microbiome

Commentary: Microbiomes: Curating communities from plants – Gwyn A. Beattie – Nature

Better link than yesterday: Functional overlap of the Arabidopsis leaf and root microbiota – Yang Bai – Nature

Bioinformatics and metagenomics

A New Approach for Scalable Analysis of Microbial Communities – Ehsaneddin Asgari – ArXiv

Microbial ecology

Networks of energetic and metabolic interactions define dynamics in microbial communities – Mallory Embree

Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria – João Barroso-Batista – Nature Communications

Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils – Christina Kaiser – Nature Communications

Proteomics

Enhancing Metaproteomics – The value of models and defined environmental microbial systems – Florian-Alexander Herbst – Proteomics

Infection microbiology

Nature Supplement: Expanding the role of diagnostic and prognostic tools for infectious diseases in resource-poor settings – Azra C. Ghani – Nature

Microbes in the news

Bacteriophage therapy: an alternative to antibiotics? An interview with Professor Martha Clokie – April Cashin-Garbutt – News Medical

Friends for Life: How Good Bugs Keep You Healthy (Op-Ed) – Jeremy Taylor – LiveScience

Science, publishing, and career

How to build a better PhD: There are too many PhD students for too few academic jobs — but with imagination, the problem could be solved – Julie Gould – Nature

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