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.

Wishing you all happy holidays / Merry Christmas!

Events

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

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.

Stanford University unexpectedly shut down my email account a couple of days ago. Of course I knew that was going to happen eventually when you leave work. But I had assumed that I would get a couple of months continued email access, like all my other coworkers got who left the university. I had checked with several others, but they all got 6 or 12 months extension without any problems.

Alas, I am not getting the same privileges, and so I have no way to contact collaborators, access and finish due peer reviews, or continue to mentor that high school student. I am trying to change all the many accounts that I have, but there are probably many that I cannot remember right now.

So here is my gmail address, in case you want to reach out to me. I deeply apologize to whatever journal is still waiting for my peer review!

Elisabeth Bik, previously Stanford University, now working at uBiome.

Several microbiome-related papers in Cell this week, Candida in kids’ saliva, two middle ear microbiome papers, yeasts in vineyards, and a database of viruses.

General microbiome

Cell has a microbiome special this week:

Review: The Central Nervous System and the Gut Microbiome – Gil Sharon
Colonic Crypt Protects Stem Cells from Microbiota-Derived Metabolites – Gerard E. Kaiko
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity – Melanie Schirmer
Host and Environmental Factors Influencing Individual Human Cytokine Responses – Rob ter Horst
A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans – Yang Li

How multi-partner endosymbioses function – Angela E. Douglas – Nature Reviews Microbiology

Human oral microbiome

Prevalence of Candida albicans and carriage of Candida non-albicans in the saliva of preschool children, according to their caries status – Carla Paola Lozano Moraga – Acta Odontologica Scandinavica

Nutritional Correlates of Human Oral Microbiome – Ikuko Kato – Journal of the American College of Nutrition

Human respiratory microbiome

Respiratory Syncytial Virus Bronchiolitis: Enter the Microbiome – James E. Gern – American Journal of Respiratory and Critical Care Medicine

Human skin and ear microbiome

Middle ear microbiome differences in indigenous Filipinos with chronic otitis media due to a duplication in the A2ML1 gene – Regie Lyn P. Santos-Cortez – Infectious Diseases of Poverty

Identification of the Bacterial Reservoirs for the Middle Ear Using Phylogenic Analysis – Chun Ling Chan – JAMA Otolaryngol Head Neck Surg.

Human gut microbiome

Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status – Monica Di Paola – Frontiers in Microbiology

Phylogenetic profile of gut microbiota in healthy adults after moderate intake of red wine – Elvira Barroso – Molecular Nutrition & Food Research

Review: Targeting gut microbiota: a potential promising therapy for diabetic kidney disease – Zhonge Chen – Am J Transl Res

Microbes in human blood

The plasma virome of febrile adult Kenyans shows frequent parvovirus B19 infections and a novel arbovirus (Kadipiro virus) – Carolyne Ngoi – Journal of General Virology

Animal experiments

Responses of earthworms and microbial communities in their guts to Triclosan – Lili Ma – Chemosphere

Animal microbiome

Gradual Changes of Gut Microbiota in Weaned Miniature Piglets – Jun Hu – Frontiers in Microbiology

Mussels: Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis – Ruby Ponnudurai – the ISME Journal

Sponges: Archaeal and bacterial communities of Xestospongia testudinaria and sediment differ in diversity, composition and predicted function in an Indonesian coral reef environment – Ana Rita Moura Polónia – Journal of Sea Research

The Origin of Mucosal Immunity: Lessons from the Holobiont Hydra – Katja Schröder – mBio

Plant, root, and soil microbiome

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature – Marc D. Auffret – PLOS ONE

Review: Yeasts found in vineyards and wineries – Cristian Varela – Yeast

Water microbiome

Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River – Jayaraman Suriya – Applied Microbiology and Biotechnology

Book chapter: Anaerobic Microbial Communities and Processes Involved in the Methane Cycle in Freshwater Lakes-a Focus on Lake Pavin – Anne-Catherine Lehours – Lake Pavin

Book chapter: Study of Prokaryotes and Viruses in Aquatic Ecosystems by Metagenetic and Metagenomic Approaches – Gisèle Bronner – Lake Pavin

Review: Quorum Sensing in Marine Microbial Environments – Laura R. Hmelo – Annual Review of Marine Science

Review: SAR11 Bacteria: The Most Abundant Plankton in the Oceans – Stephen J. Giovannoni – Annual Review of Marine Science

Phages and viruses

Pharmacometabolomics Informs Viromics toward Precision Medicine – Angeliki Balasopoulou – Frontiers in Pharmacology

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses – David Paez-Espino – Nucleic Acids Research

Metagenomics and bioinformatics

Evaluating and Optimizing the Performance of Software Commonly Used for the Taxonomic Classification of DNA Metabarcoding Sequence Data – Rodney T. Richardson – Molecular Ecology Resources

Metabolomics

Experimental Evolution of Metabolic Dependency in Bacteria – Glen D’Souza – PLOS Genetics

Microbes in the news

Well-Fed Microbiome Cookbook Update – Kristina Campbell – The Intestinal Gardener

Researcher studying squid-human bacteria connection – Southern Illinois University

Discovery of new bacteria complicates problem with salmon poisoning in dogs – Phys.org

VIDEO: Gut microbiome key influencer of weight, metabolic syndrome – Healio

18min podcast: Harvesting the Aquatic Microbiome for New Drugs – The BioReport

Microbes and the market

Go with the gut – at uBiome Inc., science meets business opportunity – The Globe and Mail

Listen To Your Gut – JentleBiz

The health test that could transform your wellbeing – for just £279 – The Telegraph