December 30, 2016

Vancomycin treatment preceding fecal transplantation, a diet for IBD, dieting and gut microbiome diversity, halotolerant extremophiles for recycling pollutants, mass spectrometry on medical swabs.

Human vaginal microbiome

Genital injury signatures and microbiome alterations associated with depot medroxyprogesterone acetate usage and intravaginal drying practices – Kenzie D. Birse – The Journal of Infectious Diseases

Human gut microbiome

Oral Vancomycin Followed by Fecal Transplantation Versus Tapering Oral Vancomycin Treatment for Recurrent Clostridium difficile Infection: An Open-Label, Randomized Controlled Trial – Susy S. Hota – Clinical Infectious Diseases

Fecal Fixation: Fecal Microbiota Transplantation for Clostridium difficile Infection – Stuart Johnson – Clinical Infectious Diseases

SCD diet: Clinical and Fecal Microbial Changes With Diet Therapy in Active Inflammatory Bowel Disease – David L. Suskind – Journal of Clinical Gastroenterology

Press: Changes With Diet Therapy in Active Inflammatory Bowel Disease – Science Daily

Review: From bugs to brains: The microbiome in neurological health – Kyla A. McKay – Multiple Sclerosis and Related Disorders

Animal experiments

Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions – Nicholas W. Griffin – Cell Host & Microbe

Press: Your Crappy American Diet Might Leave Your Gut Bacteria Stunted – Ryan F. Mandelbaum – Gizmodo
Your microbiota’s previous dining experiences may make new diets less effective – EurekAlert

Intestinal Serotonin Transporter Inhibition by Toll-Like Receptor 2 Activation. A Feedback Modulation – Eva Latorre – PLOS ONE

Press: Gut microorganisms affect our physiology – EurekAlert

Alterations in the gut microbiota can elicit hypertension in rats – Sareema Adnan – Physiological Genomics

Plant, root, and soil microbiome

Impact of plant growth-promoting rhizobacteria on root colonization potential and life cycle of Rhizophagus irregularis following co-entrapment into alginate beads -P. Loján – Journal of Applied Microbiology

Review: Soil Bacteria Alter Plant Physiology to Mitigate Salinity Stress Effects in Glycophytes – Ramalingam Radhakrishnan – Frontiers in Plant Science

Presentation abstract: Soil microbial community structures and activities in relation to nitrogen cycling in two contrasting soils in Malawi – community responses to added carbon – Akane Chiba – International Nitrogen Initiative

Waste and pollution microbiology

Pyrosequencing reveals microbial community dynamics in integrated simultaneous desulfurization and denitrification process at different influent nitrate concentrations
– Chuan Chen – Chemosphere

Microbiological water quality in the medical device industry in Italy – Emilio D’Ugo – Microchemical Journal

Halotolerant extremophile bacteria from the Great Salt Lake for recycling pollutants in microbial fuel cells – Matteo Grattieri – Journal of Power Sciences

Functionality of microbial communities in constructed wetlands used for pesticide remediation: Influence of system design and sampling strategy – Tao Lv – Water Research

Metagenomic Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments as Revealed by Functional Taxonomic Strategies – Arghya Mukherjee – bioRxiv

Food microbiology

Saccharomyces uvarum is Responsible for the Traditional Fermentation of Apple CHICHA in Patagonia – ME Rodríguez – FEMS Yeast Research


Medical swab analysis using desorption electrospray ionization mass spectrometry (DESI-MS) – a non-invasive approach for mucosal diagnostics – Pamela Pruski – Analytical Chemistry

Coping with inevitable accidents in metabolism – Antoine Danchin – Microbial Biotechnology


Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing – Morag Taylor – Journal of Clinical Pathology

Microbes in the news

Short podcast: Academic Minute – Diversifying Your Microbiome. Jack Gilbert details how the sharing of bacteria from person to person could make us healthier in the long run. – Inside Higher Ed

Ancient ‘Eternal Life’ bacteria leaves Russian scientist ‘Illness-Free’ – Harry Walker – Express

Bacteria evolution offers insights into human protein interactions – Brooks Hays – UPI

High school students discover new phages: Genomics research gives youth a leg up on education – Tonya S. Grace – Kentucky New Era

Fermentation expert Sandor Katz on why we shouldn’t fear bacteria – Andrew Sun – SCMP

Novel diet therapy helps children with crohn’s disease and ulcerative colitis reach remission – Science Daily

Prebiotics for your skin: The La Roche-Posay Toleriane Double Repair Moisturizer Could Be the Secret to Better Skin – Sarah Kinonen – Allure

December 29, 2016

A foundational coral, bacteria in tree hollows, mining and visualizing microbiome data with Calypso, viral metagenomics in aquaculture.

General microbiome

Editorial: You are not alone – M. Ludwig – Acta Physiologica

Human ear microbiome

The Relationship of the Middle Ear Effusion Microbiome to Secretory Mucin Production in Pediatric Patients with Chronic Otitis Media – Krueger, Anna – The Pediatric Infectious Disease Journal

Animal experiments

Improvement of Intestinal Immune Cell Function by Lactic Acid Bacteria for Dairy Products – Tomonori Kamiya – Microorganisms

In poultry: Zeolite food supplementation reduces abundance of enterobacteria – Tanka P. Prasai – Microbiological Research

Animal microbiome

Effects of predation and nutrient enrichment on the success and microbiome of a foundational coral – Elizabeth C. Shaver – Ecology

By their own devices: invasive Argentine ants have shifted diet without clear aid from symbiotic microbes – Yi Hu – Molecular Ecology

Gut content microbiota of introduced bigheaded carps (Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe – Andrea K. Borsodi – Microbiological Research

Plant, root, and soil microbiome

Ericoid Roots and Mycospheres Govern Plant-Specific Bacterial Communities in Boreal Forest Humus – Sari Timonen – Microbial Ecology

Benzo(a)pyrene degradation and microbial community responses in composted soil – Fengxiao Zhu – Environmental Science and Pollution Research

Bacteria and Hoverflies (Diptera: Syrphidae) in Tree Hollows From the Iberian Mediterranean Forest – I. R. Sánchez-Galván – Environmental Entomology

Cd immobilization and reduced tissue Cd accumulation of rice (Oryza sativa wuyun-23) in the presence of heavy metal-resistant bacteria – Ya Li – Ecotoxicology and Environmental Safety

Water microbiome

Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control – Hetron M. Munang’andu – Frontiers in Microbiology

Food microbiology

Microbial Ecology Dynamics in Portuguese Broa Sourdough – João M. Rocha – Journal of Food Quality

Bioinformatics and metagenomics

Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions – Martha Zakrzewski – Bioinformatics

DACE: A Scalable DP-means Algorithm for Clustering Extremely Large Sequence Data – Linhao Jiang – Bioinformatics

A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases – Xing Chen – Bioinformatics

Measuring the diversity of the human microbiota with targeted next-generation sequencing – Francesca Finotello – Briefings in Bioinformatics

More microbiology

Collective Resistance in Microbial Communities by Intracellular Antibiotic Deactivation – Robin A. Sorg – PLOS Biology
Microbes in the news

Circadian rhythms and the microbiome – Cosmos Magazine

You Don’t Even Want To Know About Bacteria On The Space Station – Trace Dominguez – Seeker

Rabbits, Bacteria and Calcium – Carl Palazzolo – Long Beach Post

Bacteria evolving more sophisticated antibiotic resistance – Brooks Hays – UPI

Last chance to vote for the best microbiome paper of 2016

What was the best microbiome paper of 2016? I’ve started to count the votes, and the winners are starting to emerge…… We might have a surprising winner!

But the year is not yet over, and there is still a chance to vote for the best Microbiome paper of 2016. Look here for a list of some of my favorites (updated today), but you can also nominate one that I did not include. Self-nominations are totally acceptable! You can vote for only one paper, or for 2 or 3.

I will do my final count and post the results on Friday or Saturday. Vote via the poll on my previous post.

December 28, 2016

Human gut microbiome

Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling – Andrew M. Thomas – Frontiers in Cellular and Infection Microbiology

Gastrointestinal neuromuscular apparatus: An underestimated target of gut microbiota – Michele Pier Luca Guarino – World Journal of Gastroenterology

Immune Response of Healthy Adults to the Ingested Probiotic Lactobacillus casei Shirota
– L. S. Harbige – Scandinavian Journal of Immunology

Review: Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine – Alejandra V. Contreras – Frontiers in Physiology

Review: IL-17: overview and role in oral immunity and microbiome – L Abusleme – Oral Diseases

Animal experiments

Bacillus sp. QSI-1 Modulate Quorum Sensing Signals Reduce Aeromonas hydrophila Level and Alter Gut Microbial Community Structure in Fish – Shuxin Zhou – Frontiers in Cellular and Infection Microbiology

Use of Asian selected agricultural byproducts to modulate rumen microbes and fermentation – Yasuo Kobayashi – Journal of Animal Science and Biotechnology

Correlation of Gut Microbiota Composition with Resistance to Experimental Autoimmune Encephalomyelitis in Rats – Suzana Stanisavljević – Frontiers in Microbiology

Comparative Analysis of the Rats’ Gut Microbiota Composition in Animals with Different Ginsenosides Metabolizing Activity – Wei-Wei Dong – Journal of Agricultural Food Chemistry

Animal microbiome

Potential for Nitrogen Fixation in the Fungus-Growing Termite Symbiosis – Panagiotis Sapountzis – Frontiers in Microbiology

Impact and Influence of the Natural Vibrio-Squid Symbiosis in Understanding Bacterial–Animal Interactions – Mark J. Mandel and Anne K. Dunn – Frontiers in Microbiology

Plant, root, and soil microbiome

The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification – Yuan Yun – Frontiers in Microbiology

Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade-offs – Xiaofang Wang – Evolution

Review: The Plant as Metaorganism and Research on Next-Generation Systemic Pesticides – Prospects and Challenges – Zisis Vryzas – Frontiers in Microbiology

Extremophile microbiome

Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria – Marco Mangiagalli – The FEBS Journal

Outdoor and indoor microbiome

Bacterial characterization in ambient submicron particles during severe haze episodes at Ji’nan, China – Caihong Xu – Science of The Total Environment

An emerging paradox: Toward a better understanding of the potential benefits and adversity of microbe exposures in the indoor environment – J. Mensah-Attipoe – Indoor Air

Waste and pollution microbiome

Effect of the chemical composition of filter media on the microbial community in wastewater biofilms at different temperatures – Iffat Naz – RSC Advances

Phages and viruses

Inferring phage–bacteria infection networks from time-series data – Luis F. Jover – Royal Society Open Science

Microbes in the news

How hospitals, nursing homes keep lethal ‘superbug’ outbreaks secret – Deborah J. Nelson, David Rohde, Benjamin Lesser and Ryan McNeill – Reuters

Causes Of Rheumatoid Arthritis: Gum Disease Bacteria Triggers Joint Inflammation, Latest Research Suggests – Lizette Borreli – Medical Daily

Genome Sequencing Sheds Light On Shigella Outbreaks In California – Saranya Palanisamy – Tech Times

Now, dental implants that kill bacteria and anchor to bone – The Tribune India

Antibiotic resistance just became more complex – EurekAlert

How Germs, Dirt and Hookworms Can Boost Your Health – Ruben Castaneda – US News

December 27, 2016

Cockatiel microbiome, a hibernating frog, Baltic Sea, a book about starter cultures, microbial divisions of labor.

Human oral/respiratory microbiome

Mycobiome in the Lower Respiratory Tract – a Clinical Perspective – Robert Krause – Frontiers in Microbiology

Review: A Review of Analytical Techniques and Their Application in Disease Diagnosis in Breathomics and Salivaomics Research – David J. Beale – Int J Mol Sci

Human gut microbiome

Impact of Amoxicillin/Clavulanate and Autologous Fecal Microbiota Transplantation (FMT) on the Fecal Microbiome and Resistome – Christopher Bulow – Open Forum Infectious Diseases

Review: The Development of Our Organ of Other Kinds—The Gut Microbiota – Shirong Liu – Frontiers in Microbiology

Review: Food Additives and Contaminants: Effects on Human Gut Microbiota—A Review – Paula Roca-Saavedra – Preprints

Animal experiments

Generation of Germ-Free Ciona intestinalis for Studies of Gut-Microbe Interactions – Brittany A. Leigh – Frontiers in Microbiology

Review: Emerging Sponge Models of Animal-Microbe Symbioses – Lucia Pita – Frontiers in Microbiology

Animal microbiome

Exploring the methanogen and bacterial communities of rumen environments: solid adherent, fluid and epimural – Thijs De Mulder – FEMS Microbiology Ecology

Diversity of the Bacterial Microbiota of Anopheles Mosquitoes from Binh Phuoc Province, Vietnam – Chung T. Ngo – Frontiers in Microbiology

Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples – Maozhang He – Frontiers in Microbiology

* Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet – Luis David Alcaraz – PeerJ

* Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation – Francis Cheng-Hsuan Weng – BMC Genomics

Plant, root, and soil microbiome

Long-term effects of aided phytostabilization on microbial communities of metal-contaminated mine soil– Olatz Garaiyurrebaso – FEMS Microbiology Ecology

Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection – Caroline De Tender – Frontiers in Microbiology

Expanding the Repertoire of Carbapenem-Hydrolyzing Metallo-ß-Lactamases by Functional Metagenomic Analysis of Soil Microbiota – Dereje D. Gudeta – Frontiers in Microbiology

High Diversity of Planctomycetes in Soils of Two Lichen-Dominated Sub-Arctic Ecosystems of Northwestern Siberia – Anastasia A. Ivanova – Frontiers in Microbiology

Editorial: Microbiota of Grapes: Positive and Negative Role on Wine Quality – Giuseppe Spano – Frontiers in Microbiology

Aspect has a greater impact on alpine soil bacterial community structure than elevation – Jieyun Wu – FEMS Microbiology Ecology

Water and extremophile microbiome

Local Environmental Conditions Shape Generalist But Not Specialist Components of Microbial Metacommunities in the Baltic Sea – Markus V. Lindh – Frontiers in Microbiology

A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition – Wei Li – Frontiers in Microbiology

Viral induced microbial mortality in Arctic hypersaline spring sediments – Jesse Colangelo-Lillis – Frontiers in Microbiology

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study – Yulia A. Frank – Frontiers in Microbiology

Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments – Leah D. Brandt – Archaea

Waste and pollution microbiology

Temporal dynamics of microbial communities in microcosms in response to pollutants – Shuo Jiao – Molecular Ecology

Cultural heritage microbiology

Sloth: Survey of the state of conservation of the Mylodon listai (Xenarthra-Mylodontidae) skin fragment from the Pleistocene of Argentina kept at the Museum of La Plata (Argentina) – Daniela Silvana Nitiu – Ge-conservación

Food microbiology

* Book: Starter Cultures in Food Production – Barbara Speranza

Biofilm microbiome

Molecular methods resolve the bacterial composition of natural marine biofilms on galvanically coupled stainless steel cathodes – Athenia L. Oldham – Journal of Industrial Microbiology & Biotechnology

Metagenomics and bioinformatics

Characterization of Uncultured Genome Fragment from Soil Metagenomic Library Exposed Rare Mismatch of Internal Tetranucleotide Frequency – Yunpeng Liu – Frontiers in Microbiology

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys – Chao Xie – BMC Bioinformatics

More microbiology

Review: Chronic infections with viruses or parasites: breaking bad to make good – Andrew Godkin – Immunology

Biocontrol of Burkholderia cepacia complex bacteria and bacterial phytopathogens by Bdellovibrio bacteriovorus – Damian McNeely – Canadian Journal of Microbiology

Fitness Impact of Obligate Intranuclear Bacterial Symbionts Depends on Host Growth Phase – Chiara Bella – Frontiers in Microbiology

* Review: Understanding Microbial Divisions of Labor – Zheren Zhang – Frontiers in Microbiology

Microbes in the news

How Does a Fatty Acid Protect Pathogenic Bacteria Against Antibiotics? – Nicola M. Parry – Contagion Live

How Microcosms help us understand ecology – James MacDonald – JSTOR Daily

Takuji Yamada – Early cancer intervention with gut bacteria – Tokyo Tech Researchers

How Probiotics Could Help Prevent Atopic Dermatitis – Kenneth Bender – Specialty Pharmacy Times

December 26, 2016

Prevotella and host genetics’ roles in vaginal microbiota, saliva microbiota and dental caries, microbes on tree stumps, fungi in Hammams, and a new  CRISPR–Cas system.

Human oral microbiome

Exploration of bacterial species associated with the salivary microbiome of individuals with a low susceptibility to dental caries – Haruna Yasunaga – Clinical Oral Investigations

Human respiratory microbiome

Nasal Airway Microbiota Profile and Severe Bronchiolitis in Infants: A Case-Control Study – Hasegawa, Kohei – The Pediatric Infectious Disease Journal

Review: The Lung Microbiome and Airway Disease – Susan V. Lynch – Annals of the American Thoracic Society

Human bladder microbiome

Is there a link between urinary microbiota and bladder cancer? – Didier Raoult – European Journal of Epidemiology

Human vaginal microbiome

* Prevotella as a Hub for Vaginal Microbiota under the Influence of Host Genetics and Their Association with Obesity – Jiyeon Si – Cell Host & Microbe

Human gut microbiome

Differences in Metabolism of Ellagitannins by Human Gut Microbiota ex Vivo Cultures
– Jakub P. Piwowarski – Journal of Natural Products

Probiotic properties of Oxalobacter formigenes: an in vitro examination – Archives of Microbiology

The effects of administration of the Lactobacillus gasseri strain CP2305 on quality of life, clinical symptoms and changes in gene expression in patients with irritable bowel syndrome – K. Nobutani – Journal of Applied Microbiology

Review: The microbiome, immunity, and schizophrenia and bipolar disorder – Faith Dickerson – Brain, Behavior, and Immunity

Review: Emerging role of intestinal microbiota and microbial metabolites in metabolic control – Hilde Herrema – Diabetologia

Review: Microbial Dysbiosis in Common Variable Immune Deficiencies: Evidence, Causes, and Consequences – Roos-Marijn Berbers – Trends in Immunology

Review: Health benefits of fermented foods: microbiota and beyond – Maria L Marco – Current Opinion in Biotechnology

Animal experiments

Individual differences in stress vulnerability: the role of gut pathobionts in stress-induced colitis – Dominik Langgartner – Brain, Behavior, and Immunity

Impact of prebiotics on metabolic and behavioral alterations in a mouse model of metabolic syndrome – Lourdes Fernández de Cossío – Brain, Behavior, and Immunity

I assume this one was done in animals but not clear: Prenatal stress affects placental cytokines and neurotrophins, commensal microbes, and anxiety-like behavior in adult female offspring – Tamar L. Gur – Brain, Behavior, and Immunity

Animal microbiome

First characterization of viruses from freshwater snails of the genus Biomphalaria, the intermediate host of the parasite Schistosoma mansoni – Richard Galinier – Acta Tropica

Fish: Effects of microbe- and mussel-based diets on the gut microbiota in Arctic charr (Salvelinus alpinus) – Andreas Nyman – Aquaculture Reports

Plant, root, and soil microbiome

Interaction of chiral herbicides with soil microorganisms, algae and vascular plants – Muhammad Asad Ullah Asad – Science of the Total Environment

Mineral type and tree species determine the functional and taxonomic structure of forest soil bacterial communities – Y. Colin – Applied and Environmental Microbiology

* Colonization of Fungi and Bacteria in Stumps and Roots of Scots Pine after Thinning and Treatment with Rotstop – Katarzyna Kubiak – Journal of Phytopathology

Built environment microbiology

* Indoor fungal contamination of traditional public baths (Hammams) – Leyla Benammar – International Biodeterioration & Biodegradation

Waste and pollution microbiology

Alkaline Technosol contaminated by former mining activity and its culturable autochthonous microbiota – A. Šimonovičová – Chemosphere

Metagenomics and bioinformatics

New CRISPR–Cas systems from uncultivated microbes – David Burstein – Nature

A small-sample multivariate kernel machine test for microbiome association studies
– Xiang Zhan – Genetic Epidemiology

Recycler: an algorithm for detecting plasmids from de novo assembly graphs –
Roye Rozov – Bioinformatics

A general framework for association analysis of microbial communities on a taxonomic tree – Zheng-Zheng Tang – Bioinformatics

Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies – Seok-Hwan Yoon – International Journal of Systematic and Evolutionary Microbiology

Microbes in the news

Genomic sequencing illuminates recent Shigella outbreaks in CaliforniaResearchers identify genes associated with toxin production and antibiotic resistance – Science Daily

Raw meatEating so-called ‘cannibal sandwiches’ can be deadly, health official says.Consumption of uncooked beef poses a health risk – Dave Delozier – Channel3000

Ancient Chinese malaria remedy may help fight TB – Deccan Chronicle

The natural history of cheese mites – Scott Chimileski – American Society for Microbiology

The throwaway scope: A way to ditch superbugs? – Chad Terhune – Seacoast Online

Science, publishing, and career

Life Science Controversies of 2016 – Jef Akst – The Scientist

The world’s favourite lab animal has been found wanting, but there are new twists in the mouse’s tale – The Economist

December 24, 2016

Wishing you all happy holidays / Merrscreen-shot-2016-12-23-at-11-57-26-pmy Christmas!


ASM Conference on Mechanisms of Interbacterial Cooperation and Competition – March 1-4 2017, Washington, DC.

Human oral microbiome

Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis – Shareef M. Dabdoub – Scientific Reports

Human vaginal microbiome

Impact of periodic presumptive treatment for bacterial vaginosis on the vaginal microbiome among women participating in the Preventing Vaginal Infections trial – Jennifer E. Balkus – The Journal of Infectious Diseases

Review: The development of probiotics for women’s health – Gregor Reid – Canadian Journal of Microbiology

Human gut microbiome

Gut-sparing treatment of urinary tract infection in patients at high risk of Clostridium difficile infection – Christopher Staley – Journal of Antimicrobial Chemotherapy

Gastrointestinal carriage is a major reservoir of K. pneumoniae infection in intensive care patients – Claire L Gorrie – bioRxiv

Diagnosis of Pulmonary Tuberculosis and Detection of Resistance to Rifampin and Isoniazid through Direct Molecular Methods in Stool Samples – Sulaiman Ali Al Yousef – Annals of Clinical & Laboratory Science

Review: Therapeutic interventions for gut dysbiosis and related disorders in the elderly: antibiotics, probiotics or faecal microbiota transplantation? – R.C. Vemuri – Beneficial Microbes

Animal experiments

A probiotic combination attenuates experimental colitis through inhibition of innate cytokine production – M.S. Kim – Beneficial Microbes

Animal microbiome

Oysters: Streptomyces effect on the bacterial microbiota associated to Crassostrea sikamea oyster – Milagro García Bernal – Journal of Applied Microbiology

Sponges: Culturable bacterial communities associated to Brazilian Oscarella species (Porifera: Homoscleromorpha) and their antagonistic interactions – Marinella Silva Laport – Antonie van Leeuwenhoek

Plant, root, and soil microbiome

The isolation and characterization of resident yeasts from the phylloplane of Arabidopsis thaliana – Kai Wang – Scientific Reports

Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe – Ximei Zhang – ISME Journal

Review: Soil-root cross-talking: The role of humic substances – Serenella Nardi – Journal of Plant Nutrition and Soil Science

Water microbiome

Spatiotemporal Dynamics of the Bacterial Microbiota and Methanotrophic Bacteria on Lotic Cladophora glomerata (Chlorophyta) – Michael J Braus – bioRxiv

Metagenomics Analysis of Microorganisms in Freshwater Lakes of the Amazon Basin
Danyelle Toyama – Genome Announcements

Microbial metatranscriptomes from the thermally stratified Gulf of Aqaba/Eilat during summer – Dan R. Miller – Marine Genomics

Comment: The interactive microbial ocean – Corina P. D. Brussaard – Nature Microbiology

Waste and pollution microbiology

Microbial pathways of nitrogen removal in aerobic granular sludge treating domestic wastewater – Lorena B. Guimarães – Journal of Chemical Technology and Biotechnology

Electric microbes

Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes – Paul G. Dennis – Scientific Reports

Metagenomics and bioinformatics

OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units – Sarah L Westcott – bioRxiv

SSUnique: Detecting Sequence Novelty in Microbiome Surveys – Michael D. J. Lynch – mSystems

Autometa: Automated extraction of microbial genomes from metagenomes – IJ Miller – Planta Medica

Glycoside Hydrolases across Environmental Microbial Communities – Renaud Berlemont – PLOS Computational Biology

Microbiome of death

A Machine Learning Approach for Using the Postmortem Skin Microbiome to Estimate the Postmortem Interval – Hunter R. Johnson – PLOS ONE

Researchers estimate time since death using necrobiome – Science Daily

Food microbiology

High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation – Lin Yang – PLOS ONE

Microbial ecology

Virologists are “Symbionts” in Microbial Ecology – Ken Takai – Microbes and Environments

Review: Evidence for microbial local adaptation in nature – S A Kraemer – Molecular Ecology

Microbes in the news
For Young Kids’ Ear Infections, Longer Antibiotic Treatment Works Better – Katherine Hobson – NPR

(Rainin ad but cool microbiology) Simplifying environmental microbiology research – Paul Boughton – Scientist Live

Microbiomes Gain Momentum in Indiana’s Life Sciences – Inside Indiana Business

Hartwick’s Cole Earns American Society for Microbiology Fellowship – Hartwick College

The Them In Us – David L. Katz – Huffington Post

Women in Microbiome Research – an update

Thanks to many loyal readers and tweeps, I have received over a hundred more suggestions for my list of Women in Microbiome Research, and some corrections. So here is an updated list, now with the names of 379 (previously 277) research scientists and faculty women who work in the fields of microbial ecology or microbial biotechnology. Thank you all!

Go to this page for a form that you can fill out if you want to correct or add to the list.


December 23, 2016

Resistant starch diets, mass spectrometry imaging, viruses in coral health and disease, mitochondrial and chloroplast blocking clamps to identify plant-associated microbiomes, vitamin D and the gut, microbes in pores, uBiome Microbiome Impact Grant winner.

Pregnancy and early life

Starter formula enriched in prebiotics and probiotics ensures normal growth of infants and promotes gut health: a randomized clinical trial – Michael Radke – Pediatric Research

Human skin microbiome

The balance of metagenomic elements shapes the skin microbiome in acne and health – Emma Barnard – Scientific Reports

Microbiome of nearly sterile sites

Correspondence: Blood microbiota as a potential non-invasive diagnostic biomarker for liver fibrosis in severely obese patients: Choose carefully – Zongxin Ling – Hepatology

Human gut microbiome

 * Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk – Nathalie Bergeron – British Journal of Nutrition

Fecal Microbiota Transplant in Severe and Severe-Complicated Clostridium difficile: A Promising Treatment Approach – Monika Fischer – Gut Microbes

Evaluation of clinical safety and beneficial effects of stachyose-enriched α-galacto-oligosaccharides on gut microbiota and bowel function in humans – Ting Li – Food & Function

Low abundance of colonic butyrate-producing bacteria in HIV infection is associated
with microbial translocation and immune activation – Stephanie M. Dillon – AIDS

Meta-analysis: Pretreatment with antibiotics may enhance the efficacy of fecal microbiota transplantation in ulcerative colitis: a meta-analysis – A H Keshteli – Mucosal Immunology

Meta-analysis: Lower Level of Bacteroides in the Gut Microbiota Is Associated with Inflammatory Bowel Disease: A Meta-Analysis – Yingting Zhou – BioMed Research International

Viewpoint: The Microbiome and Risk for Obesity and Diabetes – Anthony L. Komaroff – JAMA

Review: The Impact of the Gut Microbiota on Humoral Immunity to Pathogens and Vaccination in Early Infancy – Quang N. Nguyen – PLOS Pathogens

Review: Microbiota and prebiotics modulate uremic toxins generation – Laetitia Koppe – Panminerva Medica

Review: Influence of nutrition therapy on the intestinal microbiome – Monika A. Krezaleka

Review: A Possible Role of Intestinal Microbiota in the Pathogenesis of Ankylosing Spondylitis – Lianjun Yang – Int J Mol Sci

Review: Food allergy and the gut – Anna Nowak-Wegrzyn – Nature Reviews Gastroenterology & Hepatology

The Gut Microbiome and the Liver, special issue of Seminars in Liver Disease with lots of reviews:


Animal experiments

Western diet induces colonic nitrergic myenteric neuropathy and dysmotility in mice via saturated fatty acid- and LPS-induced TLR4 signaling – François Reichardt – Journal of Physiology

* Vitamin D Signaling through Induction of Paneth Cell Defensins Maintains Gut Microbiota and Improves Metabolic Disorders and Hepatic Steatosis in Animal Models – Danmei Su – Frontiers in Physiology

Vitamin D Improves Gut Microbiota, Study Finds – Sci-News

Animal microbiome

* Review: The role of viruses in coral health and disease – Michael Sweet – Journal of Invertebrate Pathology

Plant, root, and soil microbiome

Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove (Kandelia obovata) Rhizosphere Environment – Zhi P. Ma – Frontiers in Microbiology

Bioaccumulation of metals in reeds collected from an acid mine drainage contaminated site in winter and spring – Lin Guo – Environmental Technology

* Identifying the plant associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery – Sara L. Jackrel – Molecular Ecology Resources

* Microbial competition in porous environments can select against rapid biofilm growth – Katharine Z. Coyte – PNAS

Water microbiome

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation – E. D. Beaton – Frontiers in Microbiology

Microbial Community of High Arsenic Groundwater in Agricultural Irrigation Area of Hetao Plain, Inner Mongolia – Yanhong Wang – Frontiers in Microbiology

Disturbance Increases Microbial Community Diversity and Production in Marine Sediments – Pierre E. Galand – Frontiers in Microbiology

Waste and pollution microbiology

Seafood-Processing Sludge Composting: Changes to Microbial Communities and Physico-Chemical Parameters of Static Treatment versus for Turning during the Maturation Stage – Iria Villa – PLOS ONE

Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly – James S Griffin – The ISME Journal


Mass Spectrometry Imaging of Complex Microbial Communities – Sage J. B. Dunham – Accounts Chemical Research


* Mitochondrial and chloroplast blocking clamps: Identifying the plant associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery – Sara L. Jackrel – Molecular Ecology Resources

Microbial ecology

Probabilistic adaptation in changing microbial environments – Yarden Katz – PeerJ

Microbes in the news

UCSF Researcher to Investigate Diabetes and the Microbiome in Filipino Populations with uBiome Microbiome Impact Grant – PR Web

An interesting year – Nature Microbiology

Microbiota: Reseeding the gut – Liam Drew – Nature

Danish researchers uncover bacteria’s secret code language – News Medical

New CRISPR-Cas Enzymes Discovered – Kerry Grens – The Scientist

Move over Cas9, CRISPR-Cas3 might hold the key to solving the antibiotics crisis – Sarah Buhr – Tech Crunch

Gut bacteria may hold key to treating autoimmune diseases – EurekAlert
The Secret To Treating Autoimmune Disease May Lie In The Gut – The Huffington Post

Science, publishing and career

The lives they lived: Ruth Hubbard. She was grateful simply to be a female biologist — until she got mad about needing to be grateful – Sara Corbett – New York Times


December 22, 2016

Hand washing and drying hygiene, wild and managed geese,  juvenile alpine plants.

uBiome blog

We’re Dreaming of a Brown Christmas + Winter Sale: Celebrate the holiday season with a flurry of festive feces factoids – Julie Taylor – uBiome blog

Human skin microbiome

Cleanliness in context: reconciling hygiene with a modern microbial perspective – Roo Vandegrift – bioRxiv

Human mouth microbiome

Oral Biofluid Biomarker Research: Current Status and Emerging Frontiers – Austin Wang – Diagnostics

Human gut microbiome

Hypothesis: The gut–brain connection: triggering of brain autoimmune disease by commensal gut bacteria – Hartmut Wekerle – Rheumatology

Animal microbiology

Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus) – Wen Wang – Microbiology Open

Application of genomic technologies to measure and monitor antibiotic resistance in animals – Jian-Qiang Su – Annals of the New York Academy of Sciences

Plant, root, and soil microbiome

Microbial activity promoted with organic carbon accumulation in macroaggregates of paddy soils under long-term rice cultivation – Yalong Liu – Biogeosciences

Ozone and Nitrogen Effects on Juvenile Subalpine Plants: Complex Interactions with Species and Colonization by Arbuscular Mycorrhizal Fungi (AMF) – Seraina Bassin – Water, Air, & Soil Pollution

Food microbiology

Developing a microbial time–temperature indicator to monitor total volatile basic nitrogen change in chilled vacuum-packed grouper fillets – Hsin-I Hsiao- Journal of Food Processing and Preservation

Waste and pollution microbiology

Biological Treatment of Landfill Leachate at Elevated Temperature in the Presence of Polyurethane Foam of Various Porosity – Justyna Koc-Jurczyk – Clean Soil Air Water

Built environment microbiology

Investigation of the microbial communities colonizing prepainted steel used for roofing and walling – Tran T. Huynh – Microbiology Open

Bioinformatics, modeling, ecology and statistics

Using rarefaction to isolate the effects of patch size and sampling effort on beta diversity – Adrian C. Stier – Ecosphere

Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons – Hong-Tai Cao – BioAssays

A review of simulation and modeling approaches in microbiology – A.I. Klimenko – Russian Journal of Genetics: Applied Research

Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere – Ryan J. Newton – Aquatic Microbial Ecology

Microbes in the news

* Book: Understanding the Gut Microbiota – Gerald W. Tannock

Scientists build bacteria-powered battery on single sheet of paper – Science Daily

Study: Manuka honey kills more bacteria than all available antibiotics – Amy Goodrich – Natural News

UT Southwestern researchers find new way to combat multidrug-resistant bacteria in burn injuries – News-Medical

Xylariaphilia. A blog about fungi, science, and art – Roo Vandegrift

Microbiomes Gain Momentum in Indiana’s Life Sciences – Kylie Veleta – Inside Indiana Business