Category Archives: Human oral

August 16, 2016

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Gut microbiome and drug metabolism, bacteria and concrete, transposons in metagenomes.

Note: My lab does not longer allow me to run this blog under work hours, so I will do all my literature searches in my free time from now on. 😦 Not sure how this will affect the contents and frequency, but this is such a sad development. My sincere apologies! I will still strive to have a good representation of the new literature in the microbiome field, even it this means I will have to prepare this post at 1 AM (as I do now)

Pregnancy and birth

Review: The human gut microbiota in perinatology and neonatology – Josef Neu – Seminars in Fetal and Neonatal Medicine

Human oral microbiome

PCR-based detection of composite transposons and translocatable units from oral metagenomic DNA – Supathep Tansirichaiya – FEMS Microbiology Letters
Animal microbiome

Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers – Maëva Perez – Applied and Environmental Microbiology

Human gut microbiome

Review: Gut Microbiome Interactions with Drug Metabolism, Efficacy and Toxicity – Ian D. Wilson – Translational Research

Plant, root, and soil microbiome

Methyl Mercury Formation in Hillslope Soils of Boreal Forests: The Role of Forest Harvest and Anaerobic Microbes – Rose-Marie Kronberg – Environmental Science & Technology

Divergent habitat filtering of root and soil fungal communities in temperate beech forests – Kezia Goldmann – Scientific Reports

Extremophile microbiome

First insight into microbial diversity and ion concentration in the Uyuni salt flat, Bolivia – Cesar A. Perez-Fernandez – Caribbean Journal of Science

Built environment microbiome

Analysis of bacterial communities in and on concrete – Julia A. Maresca – Materials and Structures

Metagenomics

Exploring divergent antibiotic resistance genes in ancient metagenomes and discovery of a novel beta-lactamase family – Nicolás Rascovan – Environmental Microbiology Reports

Microbes in the news

Book Review: Multitudes of Praises for Ed Yong’s “I Contain Multitudes” – Anne Estes – Mostly Microbes

The Slow Growth Movement – Or Why Microbiologists May Have Been Doing it All Wrong – Jeffrey Marlow – Discover Magazine

Discharge pipe could be source of bacteria at Oxford treatment plant – Zach Tyler – The Anniston Star

August 11, 2016

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Association between gut microbiome and cardiovascular disease risk, Arctic glacial surface habitats.

Human oral microbiome

Review: Discuss the role of microorganisms in the aetiology and pathogenesis of periapical disease – Vincent Aw – Australian Endodontic Journal

Human respiratory microbiome

Environmental and mucosal microbiota and their role in childhood asthma – Lena T. Birzele – Allergy

FUT2 genotype influences lung function, exacerbation frequency and airway microbiota in non-CF bronchiectasis – Steven L Taylor – Thorax

Human vaginal microbiome

Review: Vaginal Microbiota and Lubricant Use During Labor. Implications for Nursing Research, Practice, and Policy – Katie G. McElroy – SAGE Open Nursing

Human gut microbiome

Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants – Tanika N Kelly – Circulation Research

Association of Intestinal Microbiota with Metabolic Markers and Dietary Habits in Patients with Type 2 Diabetes – Yamaguchi Y. – Digestion

Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions – Mehrbod Estaki – Microbiome

Bacterial invasion of the pancreas revealed after analyses of the pancreatic cyst fluids – Vilvapathy Narayanan – bioRxiv

Review: Insights into human evolution from ancient and contemporary microbiome studies – Stephanie L Schnorr – Current Opinion in Genetics & Development

http://www.sciencedirect.com/science/article/pii/S0959437X1630096X

Review: An overview of the bacterial contribution to Crohn disease pathogenesis – Moftah H Alhagamhmad – Journal of Medical Microbiology

Animal experiments

Intestinal Microbial Metabolites Are Linked to Severity of Myocardial Infarction in Rats – Vy Lam – PLOS ONE

Gut Microbial Metabolites Fuel Host Antibody Responses – Myunghoo Kim – Cell Host & Microbe

Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc – Jawad Abed – Cell Host & Microbe

Editorial: When Mr. Fap Meets the Gals – Santosh K. Ghosh – Cell Host & Microbe

Plant, root, and soil microbiome

Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts – Phuong Thi Le – Genome Biology and Evolution

Review: Recent advances in actinorhizal symbiosis signaling – Emilie Froussart – Plant Molecular Biology

Water and extremophile microbiome

Marine and giant viruses as indicators of a marine microbial community in a riverine system – Lisa M. Dann – Microbiology Open

Linking microbial diversity and functionality of Arctic glacial surface habitats – Stefanie Lutz – Environmental Microbiology

More microbiology

Microbiology, philosophy and education – Maureen A. O’Malley – Microbiology Letters

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community – Pedro Gómez – Nature Communications

Review: Biofilms: an emergent form of bacterial life – Hans-Curt Flemming – Nature Reviews Microbiology

 

Microbes in the news

Mental Health, Free Will, and Your Microbiome – Maria Popova – BrainPickings

A grimy, black biofilm is starting to cover the Jefferson Memorial, and it can’t be killed – Michael E. Ruane – The Washington Post
NPS ready to battle grimy biofilm coating on Jefferson Memorial – Nick Iannelli – WTOP
The Jefferson Memorialome? The Jeffersonome? The Jefferson Microbiome? A biofilm by any other name … – Jonathan Eisen – MicroBEnet

Young Inventors Work On Secret Proteins To Thwart Antibiotic-Resistant Bacteria – Joe Palca – NPR Shots

DRDO developing bacteria from Antarctica to aid setting up of bio-toilets in India – India TV News

How the world’s tiniest organisms explain our evolution, our health, and our eventual demise: Interview with Ed Yong about Leeuwenhoek and microbes – Julia Belluz

Could Earth Bacteria Survive on Mars? LSU MARSLIFE Researcher Noelle Bryan Recovers Bacteria from the Stratosphere – Paige Brown Jarreau – Vimeo

Microbiology: Mob rule – Adrian Woolfson examines four books on the microbiological universe that churns within us – Nature

The social network in your gut – Wudan Yan – New Yorker

Bik’s non-microbiology Picks

Exoskeletons and economics: indoor arthropod diversity increases in affluent neighbourhoods – Misha Leong – Biology Letters

Research Highlight: Insect mix high in rich areas – Nature

Ancient DNA: Muddy messages about American migration – Suzanne McGowan – Nature

Science, publishing, and career

NIH sets new postdoc stipend levels – Maggie Kuo – Science

Kudos for female Antarctic researchers: to inspire the roughly 60% of early-career polar scientists who are women – Jan Strugnell – Nature

Nominate influential female Antarctic researchers and those involved in supporting research, both past and present, to potentially be included in Wikibomb event

August 9, 2016

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Climate change and increasing Vibrio species in North Atlantic, microbiome of the aging mouth, Antarctic soil around Little Auk colony.

Events

5th Exploring Human Host-Microbiome Interactions in Health and Disease – Welcome Genome Campus, Cambridge, UK, 7-9 September 2016

4th World Congress on Targeting Microbiota – Institut Pasteur, France, October 17-19, 2016

Hot topics in microbiology: Campden BRI conference – Campden BRI, Chipping Campden, Gloucestershire, UK, October 13-14

Today & tomorrow – live webcast – Standards for Microbiome Measurements @NIST – Jonathan Eisen – MicroBEnet

General microbiome

Note: includes 16S rRNA gene studies as well, so not metagenomic sensu stricto: An overview of major metagenomic studies on human microbiomes in health and disease – Hongfei Cui – Quantitative Biology

Brazil: A Step Forward to Empower Global Microbiome Research Through Local Leadership – Victor S. Pylro – Trends in Microbiology

Human oral microbiome

Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms – Takahiko Shiba – Scientific Reports

Oral microbial community typing of caries and pigment in primary dentition – Yanhui Li – BMC Genomics

Review: The subgingival periodontal microbiota of the aging mouth – Magda Feres – Periodonotology 2000

Human respiratory microbiome

Review: The microbiome in chronic inflammatory airway disease: A threatened species – Robin John Green – The South African Medical Journal

Review: Lung microbiome in human immunodeficiency virus infection – Homer L. Twigg IIIa – Translational Research

Human vaginal microbiome

Evaluation of the vaginal flora in pregnant women receiving opioid maintenance therapy: a matched case-control study – Alex Farr – BMC Pregnancy Childbirth

Human gut microbiome

Microbial Factors Associated with Postoperative Crohn’s Disease Recurrence – Emily K. Wright – Journal of Crohn’s and Colitis

The mucosal microbiota in a young child with severe non-Helicobacter gastritis – Geoffrey A. Preidis – Therapeutic Advances in Gastroenterology

Profile of Gut Microbiota Associated With the Presence of Hepatocellular Cancer in Patients With Liver Cirrhosis – M. Grąt – Transplantation Proceedings

Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population – Akira Andoh – Journal of Clinical Biochemistry and Nutrition

Book Chapter: The Second Brain and Possible Interactions with the Heart – Rosa Sollazzo – Psychotherapy for Ischemic Heart Disease

Infection microbiology

Comparison of methods for the identification of microorganisms isolated from blood cultures – Aydir Cecília Marinho Monteiro – Annals of Clinical Microbiology and Antimicrobials

Animal experiments

Disturbance in the Mucosa-Associated Commensal Bacteria Is Associated with the Exacerbation of Chronic Colitis by Repeated Psychological Stress; Is That the New Target of Probiotics? – Sohei Arase – PLOS ONE

Role of the Gut Microbiome in Modulating Arthritis Progression in Mice – Xiaofei Liu – Scientific Reports

Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut – Thibault G. Sana – PNAS

Animal microbiome

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards – Tiantian Ren – Molecular Ecology

The gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles – Aileen Berasategui – Molecular Ecology

Plant, root, and soil microbiome

The Arctic soil bacterial communities in the vicinity of a little auk colony – Sylwia Zielinska – Frontiers in Microbiology

Soil Fungal:Bacterial Ratios Are Linked to Altered Carbon Cycling – Ashish A. Malik – Frontiers in Microbiology

Ancient landscapes and the relationship with microbial nitrification – Sasha N. Jenkins – Scientific Reports

Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons – David W. Cleary – FEMS Microbiology Ecology

Are Epiphytic Microbial Communities in the Carposphere of Ripening Grape Clusters (Vitis vinifera L.) Different between Conventional, Organic, and Biodynamic Grapes? – Elizabeth Kecskeméti – PLOS ONE

Bacterial communities in Antarctic lichens – Chae Haeng Park – Antarctic Science

Water and extremophile microbiome

Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic – Luigi Vezzulli – PNAS

Press: We’re trashing the oceans — and they’re returning the favor by making us sick – Chris Mooney – The Washington Post
Deadly Bacteria Spread across Oceans as Water Temperatures Rise. Cholera bacteria and others arise in more places and in greater abundance – Umair Irfan – Scientific American
Warming seas linked to rise in cholera bacteria in Europe and US – Brian Owens – New Scientist

Microbial community structure in hypolentic zones of a brine lake in a desert plateau, China – Wenzhen Yuan – Environmental Earth Sciences

Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts) of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile – Ana B. Fernandez – Frontiers in Microbiology

Bioreactor microbiome

The full-scale anaerobic digestion microbiome is represented by specific marker populations – Jo De Vrieze – Water Research

Viruses and phages

Challenges in the analysis of viral metagenomes – Rebecca Rose – Virus Evolution

Metagenomics and bioinformatics

Bipartite graph analyses reveal inter-domain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins – Alexander L. Jaffe – Environmental Microbiology

FARAO – The Flexible All-Round Annotation Organizer – Rickard Hammarén – Bioinformatics

Identifying wrong assemblies in de novo short read primary sequence assembly contigs – Vandna Chawla – Journal of Biosciences

A Bayesian Framework for the Classification of Microbial Gene Activity States – Craig Disselkoen – Frontiers in Microbiology

Techniques

Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs – Martin A. Fischer – Frontiers in Microbiology

More microbiology

Editorial: New insights into microbial ecology through subtle nucleotide variation – A M. Eren – Frontiers in Microbiology

Neisseria meningitides Can Survive in Corpses for At Least Eleven Days – Antonio Osculati – Frontiers in Cellular and Infection Microbiology

Microbes in the news

List of papers about bias in microbiome techniques: The unbearable madness of microbiome – Mick Watson – Opiniomics

Book Review: Follow your gut – The Enormous Impact of Tiny Microbes – Daniel K. Morais – Frontiers in Microbiology

Brito went to Fiji to study mobile genes in human microbiome – Tom Fleischman – Cornell Chronicle

MSU graduate awarded NSF fellowship to study disease affecting world’s citrus crops – Denise Hoepfner – Montana State University

Bacteria Could Aid Search for Creatures On Other Planets – Elizabeth Howell – Astrobiology Magazine

U.Va. scientists make important discovery about dangerous bacteria strains
Researchers pinpoint mechanisms of C. difficile strains – Daisy Xu – Cavalier Daily

Did farming practices in China create an antibiotic resistant bacteria that’s spreading around the world? – Alanna Shaikh – United Nations Dispatch

Science, publishing, and career

Dog eat dog: is a troubled expedition to Kenya causing the Smithsonian to devour its young?
A star scientist stands accused of misconduct, but colleagues say he’s being railroaded
– Michael Balter – The Verge

A “Scientific Diversity” Intervention to Reduce Gender Bias in a Sample of Life Scientists – Corinne A. Moss-Racusin – CBE Life Sciences Education

Bik’s non-microbiology Picks

Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children – Michelle M. Stein – New England Journal of Medicine

August 6, 2016

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Airwair microbiome at birth, fungi on strawberries, molds in a library.

Pregnancy and birth

The Airway Microbiome at Birth – Charitharth Vivek Lal – Scientific Reports

Press: Discovery of Infants’ Airway Microbiomes May Help Predict Lung Disease
A newborn’s airway — once thought to be sterile until after birth — is colonized by bacteria– University of Alabama at Birmingham
Discovery of infants’ airway microbiomes may help predict lung disease – Jeff Hansen – Medical Xpress

Gestational Diabetes is associated with changes in Placental Microbiota and Microbiome – Judit Bassols – Pediatric Research

Human respiratory microbiome (also see Pregnancy and Birth)

Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features – Guoqin Yu – Genome Biology

High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors – Daniela Janek – PLOS Pathogens

Human ear microbiome

Molecular microbiological profile of chronic suppurative otitis media – Michel Neeff – Journal of Clinical Microbiology

Human gut microbiome

Antibiotic-Induced Gut Microbiota Disruption Decreases TNF-α Release by Mononuclear Cells in Healthy Adults – Jacqueline M. Lankelma – Clinical and Translational Gastroenterology

Review: Fecal Microbiota Transplantation and Its Usage in Neuropsychiatric Disorders – Alper Evrensel – Clinical Psychopharmacology and Neuroscience

Review: Interactions between the gut microbiome and the central nervous system and their role in schizophrenia, bipolar disorder and depression – Adrian Andrzej Chrobak – Archives of Psychiatry and Psychotherapy

Animal microbiome

Strain diversity and host specificity in a specialized gut symbiont of honey bees and bumble bees – J. Elijah Powell – Molecular Ecology

Flow cytometric enumeration of bacterial in the coral surface mucus layer – Yvan Bettarel – Journal of Microbiological Methods

Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank – Tanya Brown – PeerJ Preprint

Plant, root, and soil microbiome

Metagenomic Analysis of Fungal Diversity on Strawberry Plants and the Effect of Management Practices on the Fungal Community Structure of Aerial Organs – Ahmed Abdelfattah – PLOS ONE

The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon-availability in Mediterranean semiarid soils – Felipe Bastida – Molecular Ecology

Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem – Allison M. Veach – Molecular Ecology

Review: Phytoremediation: state-of-the-art and a key role for the plant microbiome in future trends and research prospects – Sofie Thijs – International Journal of Phytoremediation

Review: Bacterial pathogenesis of plants: future challenges from a microbial perspective. Challenges in Bacterial Molecular Plant Pathology – Sebastian Pfeilmeier – Molecular Plant Pathology

Review: Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments – Lucie Musilova – Int J Mol Sci

Water and extremophile microbiome

Unexpected biodiversity of ciliates in marine samples from below the photic zone – Jean-David Grattepanche – Molecular Ecology

Meltwater export of prokaryotic cells from the Greenland Ice Sheet – Karen A. Cameron – Environmental Microbiology

Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas – Haixia Zhou – Frontiers in MIcrobiology

Review: Extremophilic adaptations and biotechnological applications in diverse environments – James Charlesworth – AIMS Microbiology

Built environment microbiome

Detection of volatile metabolites of moulds isolated from a contaminated library – Anna Micheluz – Journal of Microbiological Methods

Review: Shoe soles as a potential vector for pathogen transmission: A systematic review – Tasnuva Rashid – Journal of Applied Microbiology

Bioinformatics and metagenomics
PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories – Victor Hanson-Smith – PLOS Computational BIology

The Phylogenetic LASSO and the Microbiome – Stephen T Rush – arXiv

Microbiome networks: A systems framework for identifying candidate microbial assemblages for disease management – Ravin Poudel – Phytopathology

Techniques

On the study of microbial transcriptomes using second- and third-generation sequencing technologies – Sang Chul Choi – Journal of Microbiology

Microbes in the news

Notre Dame Researcher Explores Bacteria beyond the Ability of Typical Hospital Setting: Gail Weaver – Nina Welding – Engineering

 

August 5, 2016

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Urinary tract microbiome, preterm gut microbiota and humanized mice, fungi of Crocus (Saffron plant), and bead-beating artefacts.

General microbiome

Introduction to special issue of Molecular Metabolism: Microbiota: ‘bugging’ insights into metabolic regulation – Thomas Schwarz-Romond – Molecular Metabolism

Human oral microbiome

Transcriptome Analysis of B Cell Immune Functions in Periodontitis: Mucosal Tissue Responses to the Oral Microbiome in Aging – Jeffrey L. Ebersole – Frontiers in Immunology

Human respiratory microbiome

Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung – Leopoldo N Segal – Thorax

Review: Microbiome in the pathogenesis of cystic fibrosis and lung transplant-related disease – Sushma K. Cribbs – Translational Research

Human urinary tract microbiome

Evaluation of the Urinary Microbiota of Women With Uncomplicated Stress Urinary Incontinence – Krystal J. Thomas-White – American Journal of Obstetrics and Gynecology

Human gut microbiome

Review: Microbiota as Mediator of Cancer Progression and Therapy – Jilian L. Pope – Translational Research

Review: The human microbiome in rheumatic autoimmune diseases: A comprehensive review – Patrick Coit – Clinical Immunology

Review: Human gut microbiota plays a role in the metabolism of drugs – Lenka Jourova – Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub

Animal experiments

Preterm infant gut microbiota affects intestinal epithelial development in a humanized gnotobiotic mouse model – Yueyue Yu – American Journal of Physiology – Gastrointestinal and Liver Physiology

Symbiotic gut commensal bacteria act as host cathepsin S activity regulators – Alex Steimle – Journal of Autoimmunity

Research Highlight (but very harsh title): Gut microbiota: Microbiota and behaviour: visiting the sins of the mother – Paul Forsythe – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research – Karina Gajardo – Scientific Reports

Plant, root, and soil microbiome

Molecular phylogeny, diversity, community structure and plant growth promoting properties of fungal endophytes associated with the corms of Saffron plant: an insight into the microbiome of Crocus sativus Linn – Zahoor Ahmed Wani – Fungal Biology

Leaf Treatments with a Protein-Based Resistance Inducer Partially Modify Phyllosphere Microbial Communities of Grapevine – Martina Cappelletti – Frontiers in Plant Science

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils – Xue Zhou – Frontiers in Microbiology

Fungus-associated bacteriome in charge of their host behavior – Kristin Schulz-Bohm – Fungal Genetics and Biology

Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control – Josefa Blaya – PLOS ONE

Water and extremophile microbiome

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris – Sonja Oberbeckmann – PLOS ONE

Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica – Heather N. Buelow – Frontiers in Microbiology

Microbial community structure shifts are associated with temperature, dispersants and nutrients in crude oil-contaminated seawaters – Long Meng – Marine Pollution Bulletin

Bioinformatics and metagenomics

Rapid resistome mapping using nanopore sequencing – Eric van der Helm – bioRxiv

Metabolomics

Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena – Jinchun Sun – Toxicology in Vitro

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future – S. Barnes – Journal of Mass Spectrometry

Techniques

Bead-beating artefacts in the Bacteroidetes to Firmicutes ratio of the human stool metagenome – Heidi C. Vebø – Journal of Microbiological Methods

Pipeline for amplifying and analyzing amplicons of the V1–V3 region of the 16S rRNA gene – Heather K. Allen – BMC Research Notes

A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics – Risa Takagi – PLOS ONE

More microbiology

Metabolic engineering of microbial competitive advantage for industrial fermentation processes – A. Joe Shaw – Science

Microbes in the news

AGA establishes NIH-funded registry to track fecal microbiota transplants – EurekAlert

Maternal microbial inheritance—benefits of breastfeeding – Md Zohorul Islam

ASM Agar Art Calendar 2016/2017

Science, publishing, and career

What Is the Key Best Practice for Collaborating with a Computational Biologist? – Cell Systems

University of Waterloo boosts salaries of female faculty after discrepancy found – Paola Loriggio – CP24

Bik’s Non-Microbiology Picks

Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits – Hagop S. Atamian – Science
How do sunflowers follow the Sun—and to what end? – Winslow R. Briggs – Science

August 4, 2016

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Human breast tissue microbes, foliar bacteria, SAR11 genomes, and a new book about babies growing up too clean.

Human oral microbiome

Oral, Intestinal, and Skin Bacteria in Ventral Hernia Mesh Implants – Odd Langbach – Journal of Oral Microbiology

A novel compound to maintain a healthy oral plaque ecology in vitro – Marleen M. Janus
– Journal of Oral Microbiology

Paper on periodontal disease by computer scientists, but no dentists involved, and no mentioning of ethics approval or informed consent…
Metagenomic Analysis and Features Selection in Human Oral Microbiota Associated with Periodontal Disease – Wen-Pei Chen – The 33rd Workshop on Combinatorial Mathematics and Computation Theory

Human skin/breast tissue microbiology

The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease – Tina J. Hieken – Scientific Reports

Press: Researchers identify breast microbiome/bacterial differences between healthy and cancerous tissue – Medical Xpress

Also contains animal experiments: Transplantation of human skin microbiota in models of atopic dermatitis – Ian A. Myles – JCI Insight

Human gut microbiome

Effects of scFOS on the composition of fecal microbiota and anxiety in patients with irritable bowel syndrome: a randomized, double blind, placebo controlled study – F. Azpiroz – Neurogastroenterology & Motility

Letter: Dyspepsia and the microbiome: time to focus on the small intestine – Laurie Zhong – Gut

Review: Exposure to inorganic arsenic can lead to gut microbe perturbations and hepatocellular carcinoma – Jonathan Choiniere – Acta Pharmaceutica Sinica B

Review: Modulation of type 1 and type 2 diabetes risk by the intestinal microbiome –
Alexandra Paun – Pediatric Diabetes

Animal experiments

Pterostilbene-induced changes in gut microbiota composition in relation to obesity – Usune Etxeberria – Molecular Nutrition & Food Research

The skin microbiome in allergen-induced canine atopic dermatitis – Felipe Pierezan – Veterinary Dermatology

Plant, root, and soil microbiome

Foliar bacteria and soil fertility mediate seedling performance: a new and cryptic dimension of niche differentiation – Eric A. Griffin – Ecology

DGGE: Effect of karst rocky desertification on soil fungal communities in Southwest China – P.C. Wang – Genetics and Molecular Research

Water and extremophile microbiome

SAR11 bacteria linked to ocean anoxia and nitrogen loss – Despina Tsementzi – Nature

Press: Global warming, a dead zone and surprising bacteria – Phys.org

Sulfate reduction and inorganic carbon assimilation in acidic thermal springs of the Kamchatka peninsula – E. N. Frolov – Microbiology

Book Chapter: Bacterial Diversity of the Boka Kotorska Bay – Sandra Jokanović – The Handbook of Environmental Chemistry

Bioinformatics and metagenomics

An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria – Stephen Nayfach – bioRxiv

Advances in the recovery of haplotypes from the metagenome – Samuel M Nicholls – bioRxiv

Techniques

Virtual microfluidics for digital quantification and single-cell sequencing – Liyi Xu – Nature Methods

Microbial Nanoculture as an Artificial Microniche – Tagbo H. R. Niepa – Scientific Reports

Considerations for optimizing microbiome analysis using a marker gene – Jacobo de la Cuesta-Zuluaga – Frontiers in Nutrition

Microbes in the news

Dirty baby: Just how clean does your child need to be? – Bill Daley – Chicago Tribune

New book: Let Them Eat Dirt. Saving Your Child From an Oversanitized World – B. Brett Finlay and Marie-Claire Arrieta

Cloud computing used to analyze microbiological samples – Tim Sandle – Digital Journal

Bacteria Show Capacity for Rapid, Beneficial Mutations – University of Texas News

Video: Vibrio cholerae swimming in the gut of a live zebrafish – Phys.org

How the microbiome will lead a revolution in the consumerization of personalized medicine and diet – Kobi Gershoni – Tech Crunch
Science, publishing, and career

Scholarly Olympics: How the games have shaped research. A graphical guide to the impact of the Olympics on science – Ramin Skibba – Nature

‘Kudos’ promises to help scientists promote their papers to new audiences
Increasingly popular social-media tool says it can maximize reach and impact of research – Jeffrey Perkel – Nature

August 3, 2016

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Saliva and Polycystic Ovary Syndrome, early colonization of honey bees, hospital air metagenomes, analysis tool for viral metagenomes.

Human oral microbiome

The Salivary Microbiome in Polycystic Ovary Syndrome (PCOS) and its Association with Disease-related Parameters: A Pilot Study – Lisa Lindheim – Frontiers in Microbiology

A novel compound to maintain a healthy oral plaque ecology in vitro – Marleen M. Janus – Journal of Oral Microbiology

Human vaginal microbiome

Does the vaginal microbiota plays a role in the development of cervical cancer? – Maria Kyrgiou – Translational Research

Human skin microbiome

Diverse human skin fungal communities in children converge in adulthood – Jay-Hyun Jo – Journal of Investigative Dermatology

Human gut microbiome

A pleiotropic missense variant in SLC39A8 is associated with Crohn’s disease and human gut microbiome composition – Dalin Li – Gastroenterology

Press: Genetic Variant Newly Linked to Crohn’s Disease Also Associated with Altered Gut Microbiome Composition – PR Web

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Review: A clinical update on the significance of the gut microbiota in systemic autoimmunity – Elizabeth C. Rosser – Journal of Autoimmunity

Review: The human gut microbiome of Latin America populations: a landscape to be discovered – Fabien Magne – Current Opinion in Infectious Diseases

Animal microbiome

Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers – Ryan S. Schwarz – PNAS

Another pika paper by the same authors (who killed all pika to obtain gut contents – booh): Pika gut may select for rare but diverse environmental bacteria – Huan Li – Frontiers in Microbiology

Review: Bacterial symbiosis in the fish gut and its role in health and metabolism – Goutam Banerjee – Symbiosis

Plant, root, and soil microbiome

Diverse gene functions in a soil mobilome – Wenting Luo – Soil Biology and Biochemistry

Genetic Diversity and Association Characters of Bacteria Isolated from Arbuscular Mycorrhizal Fungal Spore Walls – Gopal Selvakumar – PLOS ONE

Spatio-temporal variation of core and satellite arbuscular mycorrhizal fungus communities in Miscanthus giganteus – Christopher J. Barnes – Frontiers in Microbiology

DGGE: Impacts of Grazing Intensity and Plant Community Composition on Soil Bacterial Community Diversity in a Steppe Grassland – Tong-bao Qu – PLOS ONE

Book chapter: Calling in the Dark: The Role of Volatiles for Communication in the Rhizosphere – Nicole M. van Dam – Deciphering Chemical Language of Plant Communication

Book Chapter: Truffle-Associated Bacteria: Extrapolation from Diversity to Function – Elena Barbieri – True Truffle (Tuber spp.) in the World

Water and extremophile microbiome

Yeasts from sub-Antarctic region: biodiversity, enzymatic activities and their potential as oleaginous microorganisms – A. Martinez – Extremophiles

First report of microorganisms of Caucasus glaciers (Georgia) – Nicoletta Makowska – Biologia

Species sorting along a subsidy gradient alters bacterial community stability – Mario E. Muscarella – Ecology

Air microbiome / Built environment microbiome

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes – Paula King – PLOS ONE

Bioinformatics

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies – Martin Norling – PLOS ONE

MetaCoMET: a web platform for discovery and visualization of the core microbiome – Yi Wang – Bioinformatics

More microbiology

Tempo and mode of genome evolution in a 50,000-generation experiment – Olivier Tenaillon – Nature

Press: Still changing after all these years. Long-term evolution experiment looks at genetic changes in bacteria: Richard Lenski – Science Daily

Review: Survival of the Fittest: How Bacterial Pathogens Utilize Bile To Enhance Infection – Jeticia R. Sistrunk – Clinical Microbiology Reviews

Book: Infective Endocarditis. Epidemiology, Diagnosis, Imaging, Therapy, and Prevention – Editors: Gilbert Habib – Springer

Élie Metchnikoff (1845–1916): celebrating 100 years of cellular immunology and beyond – David M. Underhill – Nature Reviews Immunology

Microbes in the news

Understanding diverse microbial communities: An interview with A. Murat Eren (Meren) – Kelle Freel – The Molecular Ecologist

Back from vacation? Your gut bacteria picked up souvenirs, too – Meredith Knight – Genetic Literacy Project

Evelo, Mayo Clinic team up to use bacteria for cancer immunotherapies – Ben Adams – Fierce Biotech

Plop into Canada’s first poop-themed dessert café next month – Heather Dockray – Mashable
Poop Dessert Cafe to open in Koreatown.Toronto is poised to get its first poop-themed café, set to open in August – The Star
First poo-themed dessert cafe set to open in Canada – Rachael Revesz – The Independent

Council agrees to trial of microbiology treatment – Lici Beveridge – Hattiesburg American

Opinion: Goals and possibilities in microbiology – Andrea Taboada – The Independent Florida Alligator

How Do Microbes Build Resistance to Metals? – Contagion

Bacteria Needed To Save Coral Reef – The Munich Eye

WATCH: Pac-Man Faithfully Recreated with Microbes – Nathaniel Scharping – Discover Magazine

 

July 29, 2016

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Bifidobacteria/Spirochaetes trade-off in Italians vs. Hadza, asthma, transferring depression with human stool to rats, sea squirts symbionts, spacial structure of biofilms, and a glowing review of Ed Yong’s book “I Contain Multitudes”.

General microbiome

Dysbiosis Across Multiple Body Sites in Critically Ill Adult Surgical Patients – Andrew Yeh – Shock

Pregnancy / human oral microbiome

Smoking, pregnancy and the subgingival microbiome – Akshay D. Paropkari – Scientific Reports

Review: An Integrated Review of Intestinal Microbiota in the Very Premature Infant – Melissa C. Dollings –  Neonatal Network

Human respiratory microbiome

Bacterial microbiota of the upper respiratory tract and childhood asthma – Martin Depner – Journal of Allergy and Clinical Immunology

Review: The role of anaerobic bacteria in the cystic fibrosis airway – Laura J. Sherrard – Current Opinion in Pulmonary Medicine

Human vaginal microbiome

Commentary: The relationship between the vaginal microbiome and human health – MR Millar – BJOG

Human gut microbiome

Variations in the Post-weaning Human Gut Metagenome Profile As Result of Bifidobacterium Acquisition in the Western Microbiome – Matteo Soverini – Frontiers in Microbiology

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations – Alessandra Riva – Environmental Microbiology

Histamine-secreting microbes are increased in the gut of adult asthma patients – Weronika Barcik – Journal of Allergy and Clinical Immunology

Dietary Supplementation with Rice Bran or Navy Bean Alters Gut Bacterial Metabolism in Colorectal Cancer Survivors – Amy M. Sheflin – Molecular Nutrition & Food Research

Four-week consumption of a Bifidobacterium bifidum strain modulates dominant intestinal bacterial taxa and fecal butyrate in healthy adults – Giorgio Gargari – Applied and Environmental Microbiology

Fecal microbiota transplantation for patients with steroid-resistant/dependent acute graft-versus-host disease of the gut – Kazuhiko Kakihana – Blood

Trial: Effect of prebiotic intake on gut microbiota, intestinal permeability and glycemic control in children with type 1 diabetes: study protocol for a randomized controlled trial – Josephine Ho – Trials

Opinion: How stable is the human gut microbiota? And why this question matters – Harald Brüssow – Environmental Microbiology

Research highlight: Microbial mobilomes differ between societies – Naomi Attar – Nature Reviews Microbiology

Review: High-Resolution Characterization of the Human Microbiome – Cecilia Noecker – Translational Research

Review: Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases – Mingming Sun – Journal of Gastroenterology

Review: The influence of gut derived CD39 regulatory T cells in CNS demyelinating disease – Javier Ochoa-Repáraz – Translational Research

Review: Fecal microbiota transplantation in inflammatory bowel disease: the quest for the holy grail – B Pigneur – Mucosal Immunology

Review: The Gut Microbiota in Immune-Mediated Inflammatory Diseases – Jessica D. Forbes – Frontiers in Microbiology

Review: Regulation of Autoimmunity by the Microbiome – Carlos R. Zárate-Bladés – DNA and Cell Biology

Animal experiments

Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat – John R. Kelly – Journal of Psychiatric Research

The microbiota contributes to CD8+ T cell activation and nutrient malabsorption following intestinal infection with Giardia – Infection and Immunity – Aleksander Keselman

Gut Microbial Membership Modulates CD4 T Cell Reconstitution and Function after Sepsis – Javier Cabrera-Perez – Journal of Immunology

Metabolite exchange within the microbiome produces compounds that influence Drosophila behavior – Caleb N. Fischer – bioRxiv

Variation in the Gut Microbiota of Termites (Tsaitermes ampliceps) Against Different Diets – Lijuan Su – Applied Biochemistry and Biotechnology

Animal microbiome

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts – Lars Schreiber – Frontiers in Microbiology

Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material – Ali H.D. Janab -Journal of Microbiological Methods

Death Becomes Them: Bacterial community dynamics and stilbene antibiotic production in Galleria mellonella cadavers killed by Heterorhabditis/Photorhabdus – Amanda C. Wollenberg – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium – German Zafra – Journal of Hazardous Materials

Water and extremophile microbiome

Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale – Amit Vikram – Microbial Ecology

Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods – Vinh D. Pham – Environmental Microbiology

Protocol: Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME – Matthieu Leray – Marine Genomics

Protocol: Sampling of Riverine or Marine Bacterial Communities in Remote Locations: From Field to Publication – Katja Lehmann – Marine Genomics

Microbes in space

Assessment of the Forward Contamination Risk of Mars by Clean Room Isolates from Space-Craft Assembly Facilities through Aeolian Transport – a Model Study – Luc van Heereveld – Origins of Life and Evolution of Biospheres

Built environment microbiome

Figures appear to show a gradual change, not a break, but: Summer holidays as break-point in shaping a tannery sludge microbial community around a stable core microbiota – Cesira Giordano – Scientific Reports

Food microbiology

Detailed analyses of the bacterial populations in processed cocoa beans of different geographic origin, subject to varied fermentation conditions – Cristian Bortolini – International Journal of Food Microbiology

Bioinformatics and metagenomics

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets – Scott C. Ritchie – Cell Systems

Techniques

The effect of DNA extraction methodology on gut microbiota research applications – Konstantinos Gerasimidis – BMC Research Notes

Biofilms

Review: Spatial structure, cooperation and competition in biofilms – Carey D. Nadell – Nature Reviews Microbiology

Microbes in the news

A glowing book review: Living in a microbial world, book review of “I Contain Multitudes The Microbes Within Us and a Grander View of Life” by Ed Yong – Susan Perkins – Science

State College of Florida, New College graduate wins microbiology award: Stephanie Morgan’s research won an award at the Small World Initiative Symposium – Bradenton Herald

Microbiology: A budding researcher creates a stir with her LIST-supported project: Camilla Hurst – Luxembourg Institute of Science And Technology (LIST)

‘Bugs’ on the subway: Monitoring the microbial environment to improve public health – Harvard

‘Nose-y’ Bacteria Could Yield A New Way To Fight Infection – Carolyn Beans – NPR

The Marine Microbiome – A treasure trove of scientific and industrial potential – Cordis Europa
Video: Revealing the Secrets of Marine Microbes: methods that are being used to isolate and culture marine microorganisms – MaCuMBA project

July 26, 2016

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The last common ancestor, pika gut microbiome, fire-fighting chemicals and soil microbiome, improved Illumina-compatible 18S rRNA primers.

Jobs

Verily (Google-associated) is looking for a Microbiome Research Associate

Pregnancy and birth

Probiotic properties of lactic acid bacteria isolated from human milk – N.A. Reis – Journal of Applied Microbiology

Human oral microbiome

High Throughput Quantitative Method for Assessing Coaggregation among Oral Bacterial Species – Elizabeth Levin-Sparenberg – Letters in Applied Microbiology

Periodontal infectogenomics: systematic review of associations between host genetic variants and subgingival microbial detection – Luigi Nibali – Journal of Clinical Periodontology

Human respiratory microbiome

Upper airway viruses and bacteria and clinical outcomes in children with cough – Kerry-Ann F. O’Grady – Pediatric Pulmonology

Human skin microbiome

Hypothesis: The skin microbiome: Is it affected by UV-induced immune suppression? – Vijaykumar Patra – Frontiers in Microbiology

Human gut microbiome

Gut microbiota-host interactions and juvenile idiopathic arthritis – Miika Arvonen – Pediatric Rheumatology

Designing fecal microbiota transplant trials that account for differences in donor stool efficacy – Scott W. Olesen – bioRxiv

Probiotics and the Microbiome in Celiac Disease: A Randomised Controlled Trial – Joanna Harnett – Evidence-Based Complementary and Alternative Medicine

Review: Links Between the Microbiome and Bone – Christopher J Hernandez – Journal of Bone and Mineral Research

Human vaginal microbiome

More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria – Sujatha Srinivasan – The Journal of Infectious Diseases

The Effects of Hormones and Vaginal Microflora on the Glycome of the Female Genital Tract: Cervical-Vaginal Fluid – Bernard J. Moncla – PLOS ONE

Review: New Systems for Studying Intercellular Interactions in Bacterial Vaginosis – Melissa M. Herbst-Kralovetz – The Journal of Infectious Diseases

Animal experiments

Lactulose differently modulates the composition of luminal and mucosal microbiota in C57BL/6J mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

American Ginseng Attenuates Colitis Associated Colon Carcinogenesis in Mice: Impact on Gut Microbiota and Metabolomics – Chong-Zhi Wang – Cancer Prevention Research

Alterations of Gut Microbiota After Roux-en-Y Gastric Bypass and Sleeve Gastrectomy in Sprague-Dawley Rats – Yikai Shao – Obesity Surgery

Animal microbiome

Diet diversity is associated with beta but not alpha diversity of pika gut microbiota – Huan Li – Frontiers in Mcrobiology

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats – Alejandra Hernandez-Agreda – mBio

Perspective: Hominid superorganisms – Julia A. Segre – Science

Plant, root, and soil microbiome

Long-term response of soil microbial communities to fire and fire-fighting chemicals –
A. Barreiro – Biology and Fertility of Soils

Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space – Varsik Martirosyan – Microbial Ecology

Lichen-associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude – Yanyan Wang – Frontiers in Microbiology

Water management impacts rice methylmercury and the soil microbiome – Sarah E. Rothenberg – Science of the Total Environment

Ecological restoration of a copper polluted vineyard: Long-term impact of farmland abandonment on soil bio-chemical properties and microbial communities – Luciano Cavani – Journal of Environmental Management

Review: Soil C and N models that integrate microbial diversity – Benjamin P. Louis – Environmental Chemistry Letters

Water and extremophile microbiome

Genomes of Abundant and Widespread Viruses from the Deep Ocean – Carolina Megumi Mizuno – mBio

Microbial communities associated with Antarctic snow pack and their biogeochemical implications – Runa Antony – Microbiological Research

Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats – André M. Comeau – Scientific Reports

Metabolomics

Review: Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health – Pamela Vernocchi – Frontiers in Microbiology

Functional foods

Review: Fermented Foods: Are They Tasty Medicines for Helicobacter pylori Associated Peptic Ulcer and Gastric Cancer? – Mydhily R. B. Nair – Frontiers in Microbiology

Bioinformatics

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF – Yingnan Cong – Scientific Reports
Exploring lateral genetic transfer among microbial genomes using TF-IDF – Yingnan Cong – Scientific Reports

Techniques

Design and Evaluation of Illumina MiSeq Compatible Primers for the 18S rRNA Gene for Improved Characterization of Mixed Microalgal Communities – Ian M. Bradley – Applied and Environmental Microbiology

More microbiology

Are multi-omics enough? – Cristina Vilanova – Nature Microbiology

Review: Bacterial Communities: Interactions to Scale – Reed M. Stubbendieck – Frontiers in Microbiology

The physiology and habitat of the last universal common ancestor – Madeline C. Weiss – Nature Microbiology

Press: Scientists find Luca, a single-cell, bacterium-like organism that is the common ancestor of all life on Earth – Andrew Griffin – Independent
Behold LUCA, the Last Universal Common Ancestor of Life on Earth – Jason Daley – Smithsonian
Our last common ancestor inhaled hydrogen from underwater volcanoes – Robert F. Service – Science
Meet Luca, the Ancestor of All Living Things – Nicholas Wade – New York Times

Microbes in the news

What your gut microbiome may be telling you – Katrina Clarke – The Record

Healthy microbiome supports antibiotic-free production – World Poultry

Charlottesville Lab to Test Microbiology of Local Breweries – NBC29

Nanostructured bacterial film makes new mortar resistant to water uptake – NanoWerk

Bik’s non-microbiology Picks

The Dutchies are still holding the top positions! A century of trends in adult human height – NCD Risk Factor Collaboration (NCD-RisC) – eLIFE

July 24, 2016

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Songbird, soil nitrogen-cycling around the world, and parasites on an ancient butt-wipe stick.

Pregnancy and birth

Dysfunctional gut microbiota and relative co-abundance network in infantile eczema – Heping Wang – Gut Pathogens

Human oral microbiome

Review: From focal sepsis to periodontal medicine: A century of exploring the role of the oral microbiome in systemic disease – Purnima S Kumar – The Journal of Physiology

Human gut microbiome

Review: The Role of the Gut Microbiome on Chronic Kidney Disease – B. Sampaio-Maia – Advances in Applied Microbiology

Review: The Microbiota, Immunoregulation, and Mental Health: Implications for Public Health – Christopher A. Lowry – Current Environmental Health Reports

Animal and other experiments

Insulin resistance, microbiota and fat distribution changes by a new model of vertical sleeve gastrectomy in obese rats – Nicola Basso – Diabetes

Establishment of microbiota in larval culture of Pacific oyster, Crassostrea gigas – Katia Asmani – Aquaculture

Changes in the structure of the microbial community associated with Nannochloropsis salina following treatments with antibiotics and bioactive compounds – Haifeng Geng – Frontiers in Microbiology

Animal microbiome
Social environment has a primary influence on the microbial and odor profiles of a chemically signaling songbird – Danielle J. Whittaker – Frontiers in Ecology and Evolution

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife – Maxime Galan – mSystems

Plant, root, and soil microbiome

Global biogeography of microbial nitrogen-cycling traits in soil – Michaeline B. Nelson – PNAS

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient – David J Eldridge – Journal of Animal Ecology

Biogeochemical drivers of microbial community convergence across actively retreating glaciers – Sarah C. Castle – Soil Biology and Biochemistry

The structure of bacterial communities along two vertical profiles of a deep colluvial soil – Marketa Sagova-Mareckova – Soil Biology and Biochemistry

Silver nanoparticles, ions and shape governing soil microbial functional diversity: nano shapes micro – Yujia Zhai – Frontiers in Microbiology

Water microbiome

Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks – Mariana P. Reis – Chemosphere

Effects of Copper, Nickel, and Sulphate from the Smelters at Sudbury, Ontario (Canada) on Microbial Communities in Lakes – Togwell A. Jackson – Geomicrobiology Journal

Archeological microbes

Early evidence for travel with infectious diseases along the Silk Road: Intestinal parasites from 2000 year-old personal hygiene sticks in a latrine at Xuanquanzhi Relay Station in China – Hui-Yuan Yeh – Journal of Archaeological Science: Reports

Press: Ancient Faeces Provide Earliest Evidence of Infectious Disease Being Carried on Silk Road – SciCasts
Ancient bottom wipers yield evidence of diseases carried along the Silk Road – Maev Kennedy – The Guardian

Built environment microbiome

Microorganisms associated with corrosion of structural steel in diverse atmospheres – Laura L. Machuca – International Biodeterioration & Biodegradation

More microbes

Individuals hospitalized with acute mania have increased exposure to antimicrobial medications – Robert Yolken – Bipolar Disorders

Metagenomics and bioinformatics

Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents – Michael R. Wilson – mSystems

Microbes in the news

Everyday chemicals may be messing up our microbiomes—but we don’t know – Beth Mole – Ars Technica
The jury is still out on whether antibacterial chemical impacts microbiome or causes resistance – Bob Yirka – Medical Xpress

Some Microbes Have Been With Us Since Before We Existed. Certain gut bacteria have evolved in parallel with apes, so that their family tree perfectly mirrors our own. – Ed Yong – The Atlantic

Plants have a microbiome just like humans — and it could transform how our food is produced – Ariel Schwartz – Tech Insider

New book: The Human Superorganism: How the Microbiome Is Revolutionizing the Pursuit of a Healthy Life – Rodney Dietert
Your Microbes, Yourself. In his new book, Rodney Dietert argues that it’s time to re-configure our relationship with germs: – Louise Fabiani – Pacific Standard

Science, publishing, and career

The Women and the Science
Rachel Ignotofsky tells the stories of 50 women in science in her fantastic new science art book – Scientific American
Women in Science: An Illustrated Who’s Who – Julie Leibach – Science Friday

Women in Science: An Illustrated Who’s Who