Not many microbiome articles today, but a good selection non the less! Dysbiosis and obesity in humans, effects of hay on suckling calfs, and MPLasso to Infer microbial association networks.

Human respiratory microbiome

The impact of persistent bacterial bronchitis on the pulmonary microbiome of children – Leah Cuthbertson – PLOS ONE

Human vaginal microbiome

The vaginal microbiome and sexually transmitted infections are interlinked: Consequences for treatment and prevention – Janneke H. H. M. van de Wijgert – PLOS Medicine

Human gut microbiome

Dysbiosis Signatures of Gut Microbiota Along the Sequence from Healthy, Young Patients to Those with Overweight and Obesity – Renyuan Gao – Obesity

The NLR Protein NLRP6 Does Not Impact Gut Microbiota Composition – Paul Lemire – Cell Reports

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Animal experiments

Effect of hay supplementation timing on rumen microbiota in suckling calves – Xueyan Lin – MicrobiologyOpen

Shaping of Intestinal Microbiota in Nlrp6- and Rag2-Deficient Mice Depends on Community Structure – Eric J.C. Gálvez – Cell Reports

Animal microbiome

Associations between Escherichia coli O157 shedding and the fecal microbiota of dairy cows – Chloe Stenkamp-Strahm – Journal of Applied Microbiology

Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals – Emma C. L. Finlayson-Trick – PLOS ONE

Plant, root, and soil microbiome

Shift of allelochemicals from Sorghum halepense in the soil and their effects on the soil’s bacterial community – Hongjuan Huang – Weed Biology and Management

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Bioinformatics

MPLasso: Inferring microbial association networks using prior microbial knowledge – Chieh Lo – PLOS Computational Biology

Quite a few papers on the gut microbiome today, in addition to coral reef microbiomes and the sinonasal microbiome.

Human respiratory microbiome

The sinonasal microbiota, neural signaling, and depression in chronic rhinosinusitis – Michael Hoggard – International Forum of Allergy & Rhinology

Human skin microbiome

Clostridia in the gut and onset of atopic dermatitis via eosinophilic inflammation – Eun Lee – Annals of Allergy, Asthma & Immunology 

Human gut microbiome

In vitro human colonic fermentation of indigestible fraction isolated from lunch menus: impact on the gut metabolites and antioxidant capacity – Victor Manuel Zamora-Gasga – International Journal of Food Sciences and Nutrition

Targeting gut microbiome: A novel and potential therapy for autism – Yongshou Yang – Life Sciences

Molecular mechanistic pathway of colo-rectal carcinogenesis associated with intestinal microbiota – Paramita Mandal – Anaerobe

Gut microbiota and obesity: implications for fecal microbiota transplantation therapy – Yongbo Kang – HORMONES

Correlation between gut microbiota and personality in adults: a cross-sectional study – Han-Na Kim – Brain, Behavior, and Immunity

Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome – Adrián Camacho-Ortiz – PLOSone

Water and extremophile microbiome

Interplay between stochastic and deterministic processes in the maintenance of alternative community states in Verrucomicrobia-dominated shallow lakes – Maria E. Llames – FEMS Microbiology Ecology

Complex interactions between potentially pathogenic, opportunistic, and resident bacteria emerge during infection on a reef-building coral – Sarah A. Gignoux-Wolfsohn – FEMS Microbiology Ecology

Bacterial community composition and diversity in Kalakuli, an alpine glacial-fed lake in Muztagh Ata of the westernmost Tibetan Plateau – Keshao Liu – FEMS Microbiology Ecology

It’s that time again, where we look back on what happened in the past year. Like last year, I thought it would be nice to choose the best microbiome papers of the year.  Here is a form where you can fill out your top 3 (#1 being the best, and – optional – your second and third choice). I will post the results on January 1, so you can vote until December 31, midnight, Pacific Time. Below the poll are a ton of ideas for papers that I thought were news-worthy. I probably forgot a lot, so feel free to add your own choice. Happy voting and all the best wishes for the New Year.

Update December 28: I have added Kiran Gurung’s favorite papers, so there are even more to choose from!

January 2017

• On the ecosystemic network of saliva in healthy young adults – Egija Zaura – The ISME Journal
• Gut Microbiome of the Canadian Arctic Inuit – Catherine Girard – mSphere
• Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change – Emma J. Sayer – Ecology and Evolution
• Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients – Na Tian – Applied and Environmental Microbiology
• Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women – Christina Gosmann – Immunity
• Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals – M. Andrea Azcarate-Peril – PNAS
• Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome – Ohad Manor – Cell Host & Microbe
• Target Intestinal Microbiota to Alleviate Disease Progression in Amyotrophic Lateral Sclerosis – Yong-guo Zhang – Clinical Therapeutics
• Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions – Qinghong Lia – mBio
• Duodenal Mucosa of Patients With Type 1 Diabetes Shows Distinctive Inflammatory Profile and Microbiota – Silvia Pellegrini – Journal of Clinical Endocrinology & Metabolism
• Morphological evolution of the mammalian cecum and cecal appendix – Heather F. Smith – Comptes Rendus Palevol
• The influence of proton pump inhibitors and other commonly used medication on the gut microbiota – Floris Imhann – Gut Microbes

February 2017

• Parkinson’s disease and Parkinson’s disease medications have distinct signatures of the gut microbiome – Erin M. Hill-Burns – Movement Disorders
• Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota – T. Harach – Scientific Reports
• Dynamics of the human gut microbiome in inflammatory bowel disease – Jonas Halfvarson – Nature Microbiology
• The enteric nervous system promotes intestinal health by constraining microbiota composition – Annah S. Rolig – PLOS Biology
• Bacterial Topography of the Healthy Human Lower Respiratory Tract – Robert P. Dickson – mBio
• Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions – Jocelyn M. Choo – mSphere
• Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes – Julia H. Kreznar – Cell Reports
• Microbial strain-level population structure and genetic diversity from metagenomes – Duy Tin Truong – Genome Research

March 2017 

• The blood DNA virome in 8,000 humans – Ahmed Moustafa – PLOS Pathogens
• The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level – Wiley Barton – Gut
• Stochastic assembly produces heterogeneous communities in the Caenorhabditis elegans intestine – Nicole M. Vega – PLOS Biology
• A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice – Tyson R. Chiaro – Science Translational Medicine
• NLRP12 attenuates colon inflammation by maintaining colonic microbial diversity and promoting protective commensal bacterial growth – Liang Chen – Nature Immunology
• Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice – Giada De Palma – Science Translational Medicine
• Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees – Kasie Raymann – PLOS Biology
• A phylogenetic transform enhances analysis of compositional microbiota data – Justin D Silverman – eLIFE
• Respiratory Microbiome of Endangered Southern Resident Killer Whales and Microbiota of Surrounding Sea Surface Microlayer in the Eastern North Pacific – Stephen A. Raverty – Scientific Reports
• Complex pectin metabolism by gut bacteria reveals novel catalytic functions – Didier Ndeh – Nature

April 2017

• A geographically-diverse collection of 418 human gut microbiome pathway genome databases – Aria S. Hahn – Scientific Data
• Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens – Yun-Gi Kim – Science
• Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms – Daniella Gat – Environmental Science & Technology
• Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum – Chihaya Yamada – Cell Chemical Biology
• Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome – Dorottya Nagy-Szakal – Microbiome
• Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome – Weston R. Whitaker – Cell
• Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut – Bentley Lim – Cell
• Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios – Hein M. Tun – Microbiome
• Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics – Aurian P. García-González – Cell
• A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping –
  Hyunwook Koh – Microbiome

May 2017

• Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug – Hao Wu – Nature Medicine
• Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome – Jennifer S. Labus – Microbiome
• Bacterial colonization and succession in a newly opened hospital – Simon Lax – Science Translational Medicine
• Endothelial TLR4 and the microbiome drive cerebral cavernous malformations – Alan T. Tang – Nature
• Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome – Pia S. Pannaraj – JAMA Pediatrics
• Systemic sclerosis is associated with specific alterations in gastrointestinal microbiota in two independent cohorts – Elizabeth R Volkmann – BMJ Open Gastroenterology
• Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases – Ashwin N. Ananthakrishnan – Cell Host & Microbe
• Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding – Zehra Esra Ilhan – The ISME Journal
• Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: A Pilot Study in Patients With Irritable Bowel Syndrome –  
  Maria Ines Pinto-Sanchez – Gastroenterology
• Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation – David T Riglar – Nature Biotechnology

June 2017

• Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses – Tal Korem – Cell Metabolism
• Vaginal bacteria modify HIV tenofovir microbicide efficacy in African women – Nichole R. Klatt – Science
• A Human Gut Commensal Ferments Cranberry Carbohydrates To Produce Formate – Ezgi Özcan – Applied and Environmental Microbiology
• Infant Gut Microbiome Associated With Cognitive Development – Alexander L. Carlson – Biological Psychiatry
• Extensive horizontal gene transfer in cheese-associated bacteria – Kevin S Bonham – eLIFE
• Early pregnancy vaginal microbiome trends and preterm birth – Molly J. Stout – American Journal of Obstetrics & Gynecology
• Human age and skin physiology shape diversity and abundance of Archaea on skin – Christine Moissl-Eichinger – Scientific Reports
• Microbial Genetic Composition Tunes Host Longevity – Bing Han – Cell
• Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile -Ranjit Kumar – NPJ Biofilms and Microbiomes
• Gut symbiont enhances insecticide resistance in a significant pest, the oriental fruit fly Bactrocera dorsalis– Daifeng Cheng – Microbiome
• Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils– Meng Wu – Ecotoxicology and Environmental Safety
• Disease Suppressive Soils: New Insights from the Soil Microbiome– Daniel Schlatter – Phytopathology
• Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species– Haruna et al. – Microbial Ecology
• Bacteria-mediated hypoxia functions as a signal for mosquito development – Kerri Coon – PNAS
• Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere– Qing-Lin Chen – Environmental Science & Technology
• Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome– Eugeni Belda – Scientific Reports
• Social odours covary with bacterial community in the anal secretions of wild meerkats– Sarah Leclaire – Scientific Reports

July 2017

• The Skin Microbiome of Cohabiting Couples – Ashley A. Ross – mSystems
• Penile Anaerobic Dysbiosis as a Risk Factor for HIV Infection – Cindy M. Liu – mBio
• Early-life disruption of amphibian microbiota decreases later-life resistance to parasites – Sarah A. Knutie – Nature Communications
• Skin microbiota in frogs from the Brazilian Atlantic Forest: Species, forest type, and potential against pathogens – Ananda Brito de Assis – PLOS ONE
• Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity – E Xiao – Cell Host & Microbe
• Exposure to the leaf litter microbiome of healthy adults protects seedlings from pathogen damage– Natalie Christian – Proceedings of the Royal Society B
• Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring – Jun Miyoshi – Cell Reports
• Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing – Michael Tessler – Scientific Reports
• Cutaneous Leishmaniasis Induces a Transmissible Dysbiotic Skin Microbiota that Promotes Skin Inflammation – Ciara Gimblet – Cell Host & Microbe
• Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants– Cristopher A Boya P – Scientific Reports
• Strategies for managing rival bacterial communities: lessons from burying beetles.
• Kilner RM. Journal of Animal Ecology
• Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface– Lily Momper – Environmental Microbiology Reports
• The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition– Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology
• Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin– Ana V. Longo – Molecular Ecology
• Early-Life Diet Affects Host Microbiota and Later-Life Defenses Against Parasites in Frogs – Sarah A. Knutie – Integrative & Comparitive Biology

August 2017

• The microbial metabolite desaminotyrosine protects from influenza through type I interferon – Ashley L. Steed – Science
• Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment – Julia Fukuyama – PLOS Computational Biology
• Commensal bacteria make GPCR ligands that mimic human signalling molecules
  Louis J. Cohen – Nature
• Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
  – Samuel A. Smits – Science
• Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis – Koji Watanabe – PLOS Pathogens
• Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli L. Moss – PLOS ONE
• Breast tissue, oral and urinary microbiomes in breast cancer – Hannah Wang – Oncotarget
• Microbial regulation of microRNA expression in the amygdala and prefrontal cortex – Alan E. Hoban – Microbiome
• The US National Mall Microbiome: A Census of Rhizosphere Bacteria Inhabiting Landscape Turf – Jo Anne Crouch – Crop Science
• Environmental drivers of a microbial genomic transition zone in the ocean’s interior – Daniel R. Mende – Nature Microbiology
• Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila – Adam Chun-Nin Wong – Current Biology
• Two Gut-Associated Yeasts in a Tephritid Fruit Fly have Contrasting Effects on Adult Attraction and Larval Survival– AM Piper – J Chem Ecol.
• Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome– CG Becker – Proc Biol Sci.
• Cheating and resistance to cheating in natural populations of the bacterium Pseudomonas fluorescens– John B. Bruce – Evolution
• Transition of the intestinal microbiota of cats with age– Hiroaki Masuoka – PLoS ONE
• Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring – Shantanu P. Shukla, Molecular Ecology
• Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata– Casper N. Kamutando, Scientific Reports
• Assessment of Cultivable Oral Bacterial Flora from Important Venomous Snakes of India and Their Antibiotic Susceptibilities– IK Shaikh – Current Microbiology

September 2017

• Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA – Mark Kowarsky – PNAS
• The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young – Gaorui Bian – mSphere
• Mating in the Closest Living Relatives of Animals Is Induced by a Bacterial Chondroitinase – Arielle Woznica – Cell
• Strains, functions and dynamics in the expanded Human Microbiome Project – Jason Lloyd-Price – Nature
• The intestinal microbiota regulates body composition through NFIL3 and the circadian clock – Yuhao Wang  – Science
• A secreted antibacterial neuropeptide shapes the microbiome of Hydra – René Augustin – Nature Communications
• Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention – M F Hjorth – International Journal of Obesity
• Cesarean Section, Formula Feeding, and Infant Antibiotic Exposure: Separate and Combined Impacts on Gut Microbial Changes in Later Infancy – Farzana Yasmin – Frontiers in Pediatrics
• Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women – Benjamin J. Callahan – PNAS
• The Human Salivary Microbiome Is Shaped by Shared Environment Rather than Genetics: Evidence from a Large Family of Closely Related Individuals – Liam Shaw – mBio
• The interactions between gut microbiota and entomopathogenic fungi: a potential approach for biological control of Blattella germanica (L.)– Fan Zhang, Pest Management Science
• Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata.– KH Sharp – Microbiome
• Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars–  S Chaturvedi – Scientific Reports
• Brevibacillus laterosporus isolated from the digestive tract of honeybees has high antimicrobial activity and promotes growth and productivity of honeybee’s colonies– JM Khaled – Environmental Science and Pollution Research
• Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life – Donovan H. Parks – Nature Microbiology

October 2017

• Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation – Koji Atarashi – Science
• A Gut Microbial Mimic that Hijacks Diabetogenic Autoreactivity to Suppress Colitis – Roopa Hebbandi Nanjundappa – Cell
• Indoor microbiota in severely moisture damaged homes and the impact of interventions – Balamuralikrishna Jayaprakash – Microbiome
• The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls – Sian M.J. Hemmings – Psychosomatic Medicine
• Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring – Amy Apprill – mSystems
• Household triclosan and triclocarban effects on the infant and maternal microbiome – Jessica V Ribado – EMBO Molecular Medicine
• High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut – Timothy Heisel – mSphere
• Towards a balanced view of the bacterial tree of life – Frederik Schulz – Microbiome
• Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients – Arthur E. Frankel – Neoplasia
• Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data – Fanny Berglund – Microbiome
• Root and rhizosphere bacterial phosphatase activity varies with tree species and soil phosphorus availability in Puerto Rico tropical forest– Kristine Grace Cabugao – Frontiers in Plant Science
• Do host-associated gut microbiota mediate the effect of an herbicide on disease risk in frogs?– SA Knutie – Journal of Animal Ecology
• Exploring the earthworm gut as model for soil microbial ecology– Fatima Hussain, MBL
• Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring– Amy Apprill – mSystems
• Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition– Srisailam Marupakula – Environmental Microbiology
• Nutritional immunology: Diversification and diet-dependent expression of antimicrobial peptides in the black soldier fly Hermetia illucens– H Vogel – Developmental & Comparative Immunology
• Towards standards for human fecal sample processing in metagenomic studies – Paul I Costea – Nature Biotechnology
• Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software – Alexander Sczyrba – Nature Methods

November 2017

• A communal catalogue reveals Earth’s multiscale microbial diversity – Luke R. Thompson – Nature
• A role for bacterial urease in gut dysbiosis and Crohn’s disease – Josephine Ni – Science Translational Medicine
• Human microbiome signatures of differential colorectal cancer drug metabolism – Leah Guthrie – NPJ Biofilms and Microbiomes
• Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients – V. Gopalakrishnan – Science
• The gut mycobiome of the Human Microbiome Project healthy cohort – Andrea K. Nash – Microbiome
• Foliar microbiome transplants confer disease resistance in a critically-endangered plant – Geoffrey Zahn – PeerJ
• Spontaneous body contractions are modulated by the microbiome of Hydra – Andrea P. Murillo-Rincon – Scientific Reports
• Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey – Liping Ma – Microbiome
• Quantitative microbiome profiling links gut community variation to microbial load
  Doris Vandeputte – Nature
• Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans – Jacob M. Allen – Medicine & Science in Sports & Exercise
• Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs– E. A. McKenney – Gut Microbes
• Impact of Dietary Galacto-Oligosaccharide (GOS) on Chicken’s Gut Microbiota, Mucosal Gene Expression, and Salmonella Colonization– Rebecca-Ayme Hughes – Frontiers in Veterinary Science
• Pre-print: The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ– Na Wei – bioRxiv
• Innate immune responses to metabolic stress can be detected in rumen fluids– E Trevisi – Research in Veterinary Science
• Wolbachia infection alters the relative abundance of resident bacteria in adult Aedes aegypti mosquitoes, but not larvae.– MD Audsley – Molecular Ecology
• Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome.– K Raymann – Molecular Ecology
• Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome– Kasie Raymann –  Molecular Ecology
• Relative importance of honeydew and resin for the microbial activity in wood ant nest and forest floor substrate – a laboratory study– Veronika Jílková, Soil Biology and Biochemistry
• Accessing the Hidden Microbial Diversity of Aphids: an Illustration of How Culture-Dependent Methods Can Be Used to Decipher the Insect Microbiota– Alina S. Grigorescu – Microbial Ecology
• Diets Alter the Gut Microbiome of Crocodile Lizards– Hai-Ying Jiang – Frontiers in Microbiology
• Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period– Zhigang Zhu – PLoS ONE
• The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface– J R Halliwell – Scientific Reports
• Priority effects can persist across floral generations in nectar microbial meta-communities– T Hirokazu – Oikos

December 2017

• Long-term stability in the gut microbiome over 46 years in the life of Billy Apple® – Thilini N.Jayasinghe – Human Microbiome Journal
• Subspecies in the global human gut microbiome – Paul I Costea – Molecular Systems Biology
• Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka – Amanda C. Perofsky – Proceedings of the Royal Society B
• Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation – John Beaulaurier – Nature Biotechnology
• A microbial survey of the International Space Station (ISS) – Jenna M. Lang – PeerJ
• Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data – Marius Vital – mSystems
• Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study – Maria Carmen Collado – FASEB Journal
• Moving beyond microbiome-wide associations to causal microbe identification
  – Neeraj K. Surana – Nature
• Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae) and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis– Jordan G. Kueneman – Frontiers in Microbiology
• Rhizospere yeasts improve P uptake of a maize arbuscular mycorrhizal association – Marcela Sarabia – Applied Soil Ecology
• Ammonia-oxidizing microorganisms: key players in the promotion of plant growth – Adenike Eunice Amoo – Journal of soil science and plant nutrition
• Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula.– K C Bierlich – Applied And Environmental Microbiology (DOI not available yet, so linked to PubMed)
• Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.– Miguel Carda-Diéguez – Microbiome
• Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation.– Tanzelle Oberholster – The Science Of The Total Environment
• Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization.– Aylan K Meneghine – Plos One
• Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid– Hiroki Dan – PLOS ONE
• Differential Microbial Diversity in Drosophila melanogaster: Are Fruit Flies Potential Vectors of Opportunistic Pathogens?– Luis A. Ramírez-Camejo – International Journal of Microbiology
• Comparison of the intestinal mucosal microbiota in dogs siagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment– K. Kalenyak – FEMS Microbiology Ecology
• Molecular characterization of tsetse’s proboscis and its response to Trypanosoma congolense infection– Erick O. Awuoche – PLOS Neglected Tropical Diseases
• Volatiles in the Rhizosphere: Bioprospecting for Sustainable Agriculture and Food Security– Shyamalina Haldar – In: Volatiles and Food Security. Springer
• Characterization of Bacterial Volatiles and Their Impact on Plant Health Under Abiotic Stress– Anukool Vaishnav – In: Volatiles and Food Security. Springer
• Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients –Dajana Radujković – FEMS Microbiology Ecology
• Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality– Aura Raulo – Journal of Animal Ecology
• Gut microbiota composition is associated with environmental landscape in honey bees – Julia C Jones –  Ecology and Evolution
• Evolution of microbial communities during electrokinetic treatment of antibiotic-polluted soil– Hongna Li – Ecotoxicology and Environmental Safety
• Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils– Robert Wagner – Environmental Microbiology
• Responses of soil nutrients and microbial communities to three restoration strategies in a karst area, southwest China– Dejun Li – Journal of Environmental Management
• Symbionts protect aphids from parasitic wasps by attenuating herbivore-induced plant volatiles.– Enric Frago – Nature Communications
• Antibiotic-resistant bacteria in the guts of insects feeding on plants: prospects for discovering plant-derived antibiotics.– Katarzyna Ignasiak – BMC Microbiology

Multiple articles on plant and soil microbiome, along with new BSCs (under “Water and extremophile microbiome) and some new computational methods! And a search for a microbiome core director from my thesis lab, please forward!

Events and jobs
Microbiome Core Director (Research Associate/Research Scientist) – Huttenhower Lab, Harvard T.H. Chan School of Public Health

Microbiology/Majors Biology Professor – College of the Sequoias Community College District in Visalia, CA

Pregnancy and early life
Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome – Francisco Pinto – Frontiers in Microbiology

Faecal microbiota transplant in a child with very early onset inflammatory bowel disease – Carlos Sierra Salinas – Anales De Pediatria (Barcelona, Spain : 2003)

Multi-site human microbiome
Review: Gut microbial balance and liver transplantation: alteration, management, and prediction – Xinyao Tian – Frontiers of Medicine

Human respiratory microbiome
Atopobium and Fusobacterium as novel candidates for sarcoidosis-associated microbiota. – Alexandra Zimmermann – The European Respiratory Journal

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting – Marie-Claire Arrieta – The Journal Of Allergy And Clinical Immunology

Human vaginal microbiome
High rates of bacterial vaginosis and Chlamydia in a low-income, high-population-density community in Cape Town – Katie S. Lennard – South African Journal of Science and Technology

Human gut microbiome
Subspecies in the global human gut microbiome – Paul I Costea – Molecular Systems Biology

Investigation of bioaccessibility of Cu, Fe, Mn, and Zn in market vegetables in the colon using PBET combined with SHIME. – Naiyi Yin – Scientific Reports

Improving regulation of microbiota transplants – Diane Hoffmann – Science

The Human Gut Microbial Metabolome Modulates Fungal Growth via the TOR Signaling Pathway – Carlos García – MSphere

Review: Our Gut Microbiome: The Evolving Inner Self. – Parag Kundu – Cell

Review: The gut microbiota – an emerging risk factor for cardiovascular and cerebrovascular disease – Stefanie Ascher – European Journal of Immunology

Animal experiments
Microbial communities exhibit host-species distinguishability and phylosymbiosis along the length of the gastrointestinal tract – Kevin D. Kohl – Molecular Ecology

Bile acid is a significant host factor shaping the gut microbiome of diet-induced obese mice. – Xiaojiao Zheng – Bmc Biology

Rumen Bacteria Communities and Performances of Fattening Lambs with a Lower or Greater Subacute Ruminal Acidosis Risk – Fei Li – Frontiers in Microbiology: Systems Microbiology

Dietary Antioxidant Micronutrients Alter Mucosal Inflammatory Risk in a Murine Model of Genetic and Microbial Susceptibility  – JF Pierre – The Journal of Nutritional Biochemistry

Dietary stachyose altered the intestinal microbiota profile and improved the intestinal mucosal barrier function of juvenile turbot, Scophthalmus maximus L. – Pei Yang – Aquaculture

Diversity, in-vitro virulence traits and antifungal susceptibility pattern of gastrointestinal yeast flora of healthy poultry, Gallus gallus domesticus. – Supram Hosuru Subramanya – Bmc Microbiology

Animal microbiome
Dispersal limitation promotes the diversification of the mammalian gut microbiota – Andrew H. Moeller – PNAS

Plant, root, and soil microbiome
Multiple new cryptic pathogenic Phytophthora species from Fagaceae forests in Austria, Italy and Portugal – Thomas Jung – IMA Fungus

Soil characteristics determine the rhizobia in association with different species of Mimosa in central Brazil – Raquel de Castro Pires – Plant and Soil

Effects of organochlorine pesticides on plant growth-promoting traits of phosphate-solubilizing rhizobacterium, Paenibacillus sp. IITISM08 – Rupa Rani – Environmental Science and Pollution Research

Duration of continuous cropping with straw return affects the composition and structure of soil bacterial communities in cotton fields – Lei Yang – Canadian Journal of Microbiology

The greater roles of indigenous microorganisms in removing nitrobenzene from sediment compared with the exogenous Phragmites australis and strain JS45 – Xiangqun Chi – Frontiers of Environmental Science & Engineering

Seasonal Variations in Soil and Bacteriological Properties as Affected by Phytogenic Mounds (Nebkhas) of Halocnemum strobilaceum in Lake Manzala, Egypt – Heba K. Issa – Egyptian Journal of Botany

Investigating monsoon and post-monsoon variabilities of bacterioplankton communities in a mangrove ecosystem – Anwesha Ghosh – Environmental Science and Pollution Research

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve – Min Liu – Frontiers in Microbiology

Effects of temperature, soil substrate, and microbial community on carbon mineralization across three climatically contrasting forest sites – Zuoxin Tang – Ecology and Evolution

Effects of biotic and abiotic factors on soil organic matter mineralization: Experiments and structural modeling analysis – Husen Qiu – European Journal of Soil Biology

Available forms of nutrients and heavy metals control the distribution of microbial phospholipid fatty acids in sediments of the Three Gorges Reservoir, China – Hongyan Sun – Environmental Science and Pollution Research

Temporal diversity dynamics of the arbuscular mycorrhizal fungi of Larrea tridentata (Sesse & Mocino ex DC) Coville in a semi-arid ecosystem – G Hernández-Zamudio – Revista Argentina de Microbiología (Article in Spanish)

Water and extremophile microbiome
Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality – Gregory C. A. Amos – PNAS

Molecular Mechanisms for Microbe Recognition and Defense by the Red Seaweed Laurencia dendroidea. – Louisi Souza de Oliveira – Msphere

Mycobiota of the disused ore mine of Marcinków in Śnieżnik Masiff (western Poland) – Wojciech Pusz – Journal of Mountain Science

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis. – Xue-Ping Wang – Microbiologyopen

Review: The Seagrass Holobiont and Its Microbiome – Kelly Ugarelli – Microorganisms

Built environment
PCR–DGGE Analysis on Microbial Community Structure of Rural Household Biogas Digesters in Qinghai Plateau – Rui Han – Current Microbiology

Deciphering the core fouling-causing microbiota in a membrane bioreactor: Low abundance but important roles – Shaoqing Zhang – ChemoSphere

Increasing tetracycline concentrations on the performance and communities of mixed microalgae-bacteria photo-bioreactors – Yanghui Xiong – Algal Research

Biostimulation of nutrient additions on indigenous microbial community at the stage of nitrogen limitations during composting – Huan Wang – Waste Management

Food microbiology
Mutually stimulating interactions between lactic acid bacteria and Saccharomyces cerevisiae in sourdough fermentation – S. Sieuwerts – LWT – Food Science and Technology

Review: The Mediterranean diet: metabolic and molecular mechanisms – Valeria Tosti – The Journals Of Gerontology. Series A, Biological Sciences And Medical Sciences

Probiotics / prebiotics/ antibiotics
Prebiotic Dietary Fiber and Gut Health: Comparing the in Vitro Fermentations of Beta-Glucan, Inulin and Xylooligosaccharide – Justin L Carlson – Nutrients

Review: Finding the needle in the haystack: systematic identification of psychobiotics. – Aisling Bambury – British Journal Of Pharmacology

Comment: Narrowing the spectrum: the new frontier of precision antimicrobials – Alexandra E Paharik – Genome Medicine

Bioinformatics
A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis with Microbial Compositions. – Xiang Gao – Msphere

Techniques
Amplicon sequencing of the 16S-ITS-23S rRNA operon with long-read technology for improved phylogenetic classification of uncultured prokaryotes – Joran Martijn – bioRxiv

Novel ITS1 Fungal Primers for Characterization of the Mycobiome. – Mykhaylo Usyk – Msphere

Microbes in the news
BIDMC Researchers Use Artificial Intelligence to Identify Bacteria Quickly and Accurately – Beth Israel Deaconess Medical Center

Magnetically Guided Bacteria Move Confidently Within Strong Currents, May Soon Deliver Drugs Inside Body – MedGadget

Is hand sanitizer bad for my microbiome? – Claire Maldarelli – Popular Science

Nanoparticles as a solution against antibiotic resistance? – Science Daily

Microbes on the market 
Light ‘Em Up: S&N’s Device Images Bacteria in Wounds – Nancy Crotti – MDDI

Contemplating Regulatory Frameworks for FMT – Cristi Rosa – Contagion Live

Vedanta Granted Four U.S. Patents for Therapeutics Based on Beneficial Gut Bacteria – Carolina Henriques – IBD News Today

Science, publishing, and career
What’s Responsible for the Retraction Boom? – Adam Marcus – Research Ethics in the Digital Age

Microbiology jobs and a PhD are posted today along with a review of microbiota and aging, and research looking at if/how the Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Plus a slew of other research highlights –  Enjoy!

Events and jobs

PhD: Mining and Modelling the Human Gut Microbiome to Elucidate its Metabolic Potential – Aberdeen University

Professor or Associate Professor – Medical Microbiology – University of Oslo

Part-Time Microbiology Laboratory Technician – Miami Dade College

Microbiology Laboratory Manager – Georgia Department of Public Health

General microbiome

Review: Microbiota and Aging. A Review and Commentary – Carmen García-Peña – Archives of Medical Research

 Pregnancy and early life

Influence of the intestinal microbiota on the immunogenicity of oral rotavirus vaccine given to infants in south India – Edward P.K. Parker – Vaccine

 Human respiratory microbiome

Microbial diversity within the airway microbiome in chronic pediatric lung diseases – Andrea Hahn – Infection, Genetics and Evolution

Compositional and functional variations of oral microbiota associated with the mutational changes in oral cancer – Shun-Fa Yang – Oral Oncology

 Human gut microbiome

Metabolic analysis of Panax notoginseng saponins with gut microbiota-mediated biotransformation by HPLC-DAD-Q-TOF-MS/MS – Man-Yun Chen – Journal of Pharmaceutical and Biomedical Analysis

Towards utilization of the human genome and microbiome for personalized nutrition – Stavros Bashiardes – Current Opinion in Biotechnology

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients – V. Gopalakrishnan – Science

 Animal microbiome

Co-occurrence of early gut colonization in neonatal piglets with microbiota in the maternal and surrounding delivery environments – Xue Chen – Anaerobe

 Plant, root, and soil microbiome

Ralstonia solanacearum pathogen disrupts bacterial rhizosphere microbiome during an invasion – Zhong Wei – Soil Biology and Biochemistry

Substrate-driven microbial response: A novel mechanism contributes significantly to temperature sensitivity of N2O emissions in upland arable soil – Alin Song – Soil Biology and Biochemistry

 Water and extremophile microbiome

Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture – Thorsten Stoeck – Marine Pollution Bulletin

 Probiotics / prebiotics

The Role of Prebiotics and Probiotics in Gastrointestinal Disease – Martin H. Floch – Gastroenterology Clinics of North America

Alzheimer’s disease and gut microbiota modifications: the long way between preclinical studies and clinical evidence – Cesare Mancuso – Pharmacological Research

Microbes in the news

It might be possible to remodel a baby’s microbiome (But we still don’t really know what a healthy microbiome really is) – PopularScience

Do you want to know what microbes are in the international space station? the effects of Arsenic exposure on childrens microbiomes? or perhaps you are interested in tree leaf bacterial diversity along an urban gradient?  Well, today we have it all and more! Enjoy Saturdays microbiome digest for links to the latest research on microbiomes.

General microbiome

Microbial Ecology: Community Coalescence Stirs Things Up – Matthias C. Rillig – Current Biology

Multi-site human microbiome

Distinct fecal and oral microbiota composition in human type 1 diabetes, an observational study – Pieter F. de Groot – PlosONE

Human skin microbiome

The role of the skin microbiome in atopic dermatitis: a systematic review – R.D. Bjerre – British Journal of Dermatology

Human gut microbiome

Preprint: Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls – Sudarshan A Shetty et al – BioRxiv

Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function – Noel T. Mueller et al – Genes

Correlations between gut microbiota community structures of Tibetans and geography – Daoliang Lan et al – Scientific Reports

Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh – Xiaoxi Dong – PlosONE

The role of gut microbiota in the modulation of drug action: A focus on some clinically significant issues – Diego Currò – Expert Review of Clinical Pharmacology

Review: Codevelopment of Microbiota and Innate Immunity and the Risk for Group B Streptococcal Disease – Julia Kolter – Frontiers in Immunology

Animal experiments

Glucerabacter canisensis gen. nov., sp. nov., isolated from dog feces and its effect on the hydrolysis of plant glucosylceramide in the intestine of dogs – Misho Kawata et al – Archives of Microbiology

Meta-Analysis of Fecal Microbiota and Metabolites in Experimental Colitic Mice during the Inflammatory and Healing Phases – Toshifumi Osaka – Nutrients

Animal microbiome

Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka – Amanda C. Perofsky – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity – Isabelle Laforest-Lapointe – mSystems

Microbial and Plant-Assisted Bioremediation of Heavy Metal Polluted Environments: A Review – Omena Bernard Ojuederie and Olubukola Oluranti Babalola – International Journal of Environmental Research and Public Health

Soil microbial communities of three grassland ecosystems in the Bayinbuluke, China – Keqiang Shao – Canadian Journal of Microbiology

Response of soil microbial community dynamics to Robinia pseudoacacia L. afforestation in the loess plateau: a chronosequence approach – Jinliang Liu – Plant and Soil

Microbes in space

A microbial survey of the International Space Station – Jenna M. Lang et al – PeerJ

Todays roundup of microbiome research highlights studies of wound microbiomes, the Influences of quorum-quenching probiotic bacteria (in pigs), and plant–fungal nutrient trading, to name but a few! Enjoy!

General microbiome

Gut Feeling: Researchers Are Discovering a Link Between Depression and Gut Bacteria – Mary Bates, IEEE Pulse

Human respiratory microbiome

Bacterial microbiota of the nasal passages across the span of human life – Lindsey Bomar et al, Current Opinion in Microbiology

Human skin microbiome

Development, standardization and testing of a bacterial wound infection model based on ex vivo human skin – Christoph Schaudinn et al, PLOS ONE

Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study – Lindsay Kalan et al, PLOS ONE

A dysbiotic mycobiome dominated by Candida albicans is identified within oral squamous-cell carcinomas – Manosha Perera et al, Journal of Oral Microbiology

Animal experiments

Influences of quorum-quenching probiotic bacteria on the gut microbial community and immune function in weaning pigs – Jonggun Kim et al, Animal Science Journal

Faecal microbiota in dogs with multicentric lymphoma – A. Gavazza et al, Veterinary and Comparative Oncology

Animal microbiome

Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations – Sina-Catherine Siegerstetter et al, PLOS ONE

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species – Per Eriksson et al, Infection Ecology & Epidemiology

Plant, root, and soil microbiome

Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field-grown maize roots – Peng Yu et al, New Phytologist

Role of plant–fungal nutrient trading and host control in determining the competitive success of ectomycorrhizal fungi – Sara Hortal et al, The ISME Journal

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level – Yuji Jiang et al, The ISME Journal

Habitat- and soil-related drivers of the root-associated fungal community of Quercus suber in the Northern Moroccan forest – Fatima Zahra Maghnia et al, PLOS ONE

Water and extremophile microbiome

Changes in nutrient stoichiometry, elemental homeostasis and growth rate of aquatic litter-associated fungi in response to inorganic nutrient supply – Vladislav Gulis et al, The ISME Journal

Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria – Emilie Macke et al, Nature Communications

Probiotics / prebiotics

Simulating colonic survival of probiotics in single-strain products compared to multi-strain products – S. D. Forssten et al, Microbial Ecology in Health and Disease

Bioinformatics

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication – Matthew R Olm, The ISME Journal