(post updated December 28 with some good additions suggested by voters – thank you all!

(Post open till Friday 30 December)

It’s the end of another year chockfull of microbiome papers, and I’ve seen them all! But which one do you think were the best? I’ll take nominations, and I will post the best 5 or 10 next week.

Here are some of 2016’s most discussed research papers to refresh your memories. I tried to pick a range of papers from different environments and hosts, including some very controversial ones. I also included a couple that were nominated through Twitter.

While I was going through the past Microbiome Digests from this year, I had many “Oh, yes, I forgot about that one” moments, and I hope you have those too! And, if you have not been keeping up with the literature this year, this will be a great list to start. So take a look at the list below, also think of papers I forgot to include, and vote of  your three favorite papers by using this form.

At the bottom of this post, you can vote for a maximum of three papers (unranked), and the paper(s) do not have to be on the list below. Yes, you may self-nominate (I did that too – see February). No, I will not misuse your email address!

January

• Diet-induced extinctions in the gut microbiota compound over generations – Erica Sonnenburg – Nature
• Human milk microbiota profiles in relation to birthing method, gestation and infant gender – Camilla Urbaniak – MIcrobiome
• Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels – Mason R. Stothart – Biology Letters
• Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans – Ron Sender – Cell
• The Host Shapes the Gut Microbiota via Fecal MicroRNA – Shirong Liu – Cell  Host & Microbe
• Social behavior shapes the chimpanzee pan-microbiome – Andrew H. Moeller – Science Advances
• Biogeography of a human oral microbiome at the micron scale – Jessica L. Mark Welch – PNAS

February

• Infant Gut Microbiota Development Is Driven by Transition to Family Foods Independent of Maternal Obesity – Martin Frederik Laursen – mSphere
• The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos – Felix Sommer – Cell Reports
• A Novel Microbiome Therapeutic Increases Gut Microbial Diversity and Prevents Recurrent Clostridium difficile Infection – Sahil Khanna – Journal of Infectious Diseases
• The effect of habitual and experimental antiperspirant and deodorant product use on the armpit microbiome – Julie Urban – PeerJ
• Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition – Mark R. Charbonneau – Cell
• Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea – Elisabeth M. Bik – Nature Communications

March

• Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing – Jennifer N. Patro – mSphere
• Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns – Andres Gomez – Cell Reports
• Cigarette smoking and the oral microbiome in a large study of American adults – Jing Wu – ISME Journal
• Gut microbiome–derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease – Nathan D Mathewson – Nature Immunology
• Changes in the Eye Microbiota Associated with Contact Lens Wearing – Hakdong Shin – mBio
• The maternal microbiota drives early postnatal innate immune development – Mercedes Gomez de Agüero – Science

April

• Population-level analysis of gut microbiome variation – Gwen Falony – Science
• Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity – Alexandra Zhernakova – Science
• Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle – Anastassia Gorvitovskaia – Microbiome
• Geography and Location Are the Primary Drivers of Office Microbiome Composition – John Chase – mSystems
• Helminth infection promotes colonization resistance via type 2 immunity – Deepshika Ramanan – Science
• An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis – Jun Chen – Genome Medicine
• Evaluating the diversity of soil microbial communities in vineyards relative to adjacent native ecosystems – Taylor C. Holland – Applied Soil Ecology
• Comparative genomics of Crohn’s disease-associated adherent-invasive Escherichia coli – Claire L O’Brien – Gut

May

• Genetic Determinants of the Gut Microbiome in UK Twins – Julia K. Goodrich – Cell Host & Microbe
• Dietary Shifts May Trigger Dysbiosis and Mucous Stools in Giant Pandas (Ailuropoda melanoleuca) – Candace L. Williams – Frontiers in Microbiology
• Crossover Control Study of the Effect of Personal Care Products Containing Triclosan on the Microbiome – Angela C. Poole – mSphere
• Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems
• Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems
• Temporal Stability of the Human Skin Microbiome – Julia Oh – Cell
• Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections – Maria J. Soto-Giron – Applied and Environmental Microbiology
• Ly6Chi Monocytes Provide a Link between Antibiotic-Induced Changes in Gut Microbiota and Adult Hippocampal Neurogenesis – Luisa Möhle – Cell Reports
• Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation – Hilary P. Browne – Nature

June

• Variable responses of human microbiomes to dietary supplementation with resistant starch – A. Venkataraman – Microbiome
• MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses – Vanni Bucci – Genome Biology
• Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota – Abigail P. Lauder – Microbiome
• Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment – Tiffany Hsu – mSystems
• Host species identity, site and time drive temperate tree phyllosphere bacterial community structure – Isabelle Laforest-Lapointe – Microbiome
• Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome -Ludovic Giloteaux – Microbiome
• Universality of human microbial dynamics – Amir Bashan – Nature
• Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring – Shelly A. Buffington – Cell
• Alterations of the human gut microbiome in multiple sclerosis – Sushrut Jangi – Nature Communications
• Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes – Richard Allen White III – mSystems
• Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals – Zhigang Zhang – Current Biology

July

• Microbial diversity in individuals and their household contacts following typical antibiotic courses – Shira R. Abeles – Microbiome
• Adult microbiota-deficient mice have distinct dendritic morphological changes: differential effects in the amygdala and hippocampus – Pauline Luczynski – European Journal of Neuroscience
• Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome – Robert P. Dickson – Nature Microbiology
• Cospeciation of gut microbiota with hominids – Andrew H. Moeller – Science
• Host genotype and age shape the leaf and root microbiomes of a wild perennial plant – Maggie R. Wagner – Nature Communications

August

• Uncovering Earth’s virome – David Paez-Espino – Nature
• Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome – Marc A. Sze – mBio
• Extreme Dysbiosis of the Microbiome in Critical Illness – Daniel McDonald – mSphere
• The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat – Embriette R. Hyde – mSystems
• Captivity humanizes the primate microbiome – Jonathan B. Clayton – PNAS
• The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease -Tina J. Hieken – Scientific Reports
• The Airway Microbiome at Birth – Charitharth Vivek Lal – Scientific Reports
• The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota – Ilias Lagkouvardos – Nature Microbiology

September

• Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone – Stilianos Louca – PNAS
• Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease – G. Hoarau – mBio
• Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation – Kei E Fujimura – Nature Medicine
• Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome – Erica M. Hartmann – Environmental Science & Technology
• The impact of sequence database choice on metaproteomic results in gut microbiota studies – Alessandro Tanca – Microbiome
• A reference gene catalogue of the pig gut microbiome – Liang Xiao – Nature Microbiology
• Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls – Helen Tremlett – BMC Neurology

October

• The structure and diversity of human, animal and environmental resistomes – Chandan Pal – Microbiome
• Discovery of MRSA active antibiotics using primary sequence from the human microbiome – John Chu – Nature Chemical Biology
• Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort – Antonio Gonzalez – mSystems
• Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes – Amy Apprill – mSystems
• An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
  Stephen Nayfach – Genome Research
• The effect of host genetics on the gut microbiome – Marc Jan Bonder – Nature Genetics

November

• Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History – Andrew W. Brooks – PLOS Biology
• Persistent microbiome alterations modulate the rate of post-dieting weight regain – Christoph A. Thaiss – Nature
• Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City – Holly M. Bik – mSphere
• Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities – Rafal Zgadzaj – PNAS
• A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility – Mahesh S. Desai – Cell
• Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication – Cliff S. Han – PeerJ
• Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases – Wesley Morovic – Frontiers in Microbiology
• Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome – Antoine M. Snijders – Nature Microbiology
• A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice – Hubert Plovier – Nature Medicine
• Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes – Jeremy L. Motley  – Journal of Natural Products
• Potential contribution of the uterine microbiome in the development of endometrial cancer – Marina R. S. Walther-António – Genome Medicine
• Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies – Rashmi Sinha – Cancer Epidemiology, Biomarkers & Prevention
• Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome – Hailiang Xie – Cell Systems

December

• Transmission of viruses via our microbiomes – Melissa Ly – Microbiome
• Effects of Diurnal Variation of Gut Microbes and High-Fat Feeding on Host Circadian Clock Function and Metabolism – Vanessa Leone – Cell Host & Microbe
• Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations – Christoph A. Thaiss – Cell
• Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease – Timothy R. Sampson – Cell
• Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues – Kimberly A. Krautkramer – Molecular Cell

Vote here

Nominate your favorites for Best Microbiome Papers of 2016 using this form. Rules: Vote for a maximum of 3 papers published in 2016, research papers only (no reviews), self-nominations are acceptable, and you can also nominate papers not included on the list above. I promise I will not use your email address for evil purposes 🙂