February 14, 2019

If you are feeling butterflies in your stomach today, it might not be a gut microbiome imbalance – you might’ve caught the love bug! Happy Valentines Day!  Today’s digest features some human gut/FMT studies, a few animal gut biome studies and a couple probiotic publications.  Enjoy!

General microbiome

The next step towards anticancer microbiota therapeutics – Ursula Hofer – Nature Reviews [letter]

Expanding diversity of the human microbiome – Andrea Du Toit – Nature Reviews [in brief]

FMT in the clinic – Ashley York – Nature Reviews [research highlight]

Human respiratory microbiome

Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects – Anny Camelo-Castillo – Frontiers in Microbiology

Human gut microbiome

Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome – Daniel E. Almonacid – PLoS One

[pre -print] The Human Nickel Microbiome and its relationship to Allergy and Overweight in Women – Elena Angela Lusi – bioRxiv

The Relationship between Platelet Count and Host Gut Microbiota: A Population-Based Retrospective Cross-Sectional Study – Hee-Yong Yoon – Journal of Clinical Medicine

Data-driven multiple-level analysis of gut-microbiome-immune-joint interactions in rheumatoid arthritis – QuanQiu Wang – BMC Genomics

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes – J. Alfredo Blakeley-Ruiz – BMC Microbiome

Role of the Gut Microbiome in Autism Spectrum Disorders – Joby Pulikkan – Reviews on Biomarker Studies in Psychiatric and Neurodegenerative Disorders

Faecal microbiota transplantation in Australia: bogged down in regulatory uncertainty – Samuel P. Costello – Internal Medicine Journal

Animal experiments

Characterization of oral microbiota in marmosets: Feasibility of using the marmoset as a human oral disease model – Sachiko Takehara – PLoS One

The Effect of Multispecies Probiotic Supplementation on Iron Status in Rats – Katazyna Skrypnik – Biological Trace Element Research

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples – Susakul Palakawong Na Ayudthaya – Current Microbiology

Animal microbiome

A Diverse Microbial Community Supports Larval Development and Survivorship of the Asian Tiger Mosquito (Diptera: Culicidae) – Nicholas V Travanty – Journal of Medical Entomology

Plant, root, and soil microbiome

Belowground biota responses to maize biochar addition to the soil of a Mediterranean vineyard – Pilar Andrés – Science of The Total Environment

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining – Markus Gastauer – Scientific Data

Probiotics / prebiotics

Infant Complementary Feeding of Prebiotics for the Microbiome and Immunity – Starin McKeen – Nutrients

Techniques

Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis – James B. Thissen – PLoS One

Microbes in the news

Tube pollution: Could bacteria create clean air on the London Underground?

Ed’s non-microbiology picks

Adjunctive vitamin D in tuberculosis treatment: meta-analysis of individual participant data – David A. Jolliffe – European Respiratory Journal

Physical activity protects against depression

Want Healthier Eating Habits? Start with a workout

GMO Cassava Can Provide Iron, Zinc To Malnourished African Children

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January 28, 2019

Human and General Microbiome

Book Chapter: Necrotizing Enterocolitis and the Preterm Infant Microbiome. – Jillian R. Baranowski – Part of the Advances in Experimental Medicine and Biology book series

Book Chapter: Shaping Microbiota During the First 1000 Days of Life. – Marta Selma-Royo – Part of the Advances in Experimental Medicine and Biology book series

Book Chapter: Targeting Food Allergy with Probiotics. – Lorella Paparo – Part of the Advances in Experimental Medicine and Biology book series

Review: The relation of the vaginal microbiota to early pregnancy development during In Vitro Fertilization treatment-A meta-analysis. – M. Singer – Journal of Gynecology Obstetrics and Human Reproduction

Review: Neuropeptides in the microbiota-brain axis and feeding behavior in autism spectrum disorder. – Sergueï O.Fetissov – Nutrition (Elsevier)

Review: Gut microbiome and cancer immunotherapy. – Weina Li – Cancer Letters

Review: The Microbiome-Host Interaction as a Potential Driver of Anastomotic Leak. – Victoria M. Gershuni – Current Gastroenterology Reports

Review: The links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD). – Zahra Safari – Cellular and Molecular Life Sciences

Review: The role of chronic kidney disease-associated dysbiosis in cardiovascular disease.  – Mark A Bryniarski – Experimental Biology and Medicine

Review: The Interplay between Immunity and Microbiota at Intestinal Immunological Niche: The Case of Cancer. – Rossella Cianci – International Journal of Molecular Sciences

Spotlight: Ethnicity-Influenced Microbiota: A Future Healthcare Perspective. – Madhusmita Dehingia – Trends in Microbiology

Exploration of microbiota targets for major depressive disorder and mood related traits. – Yu-Chu Ella Chung – Journal of Psychiatric Research

Altered fecal bacterial composition correlates with disease activity in inflammatory bowel disease and the extent of IL8 induction. – Farnaz Heidarian – Current Research in Translational Medicine

Metagenome – Inferred bacterial replication rates in cystic fibrosis airways. – Katarzyna Pienkowska – Journal of Cystic Fibrosis

Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus. – Jay Liu – EBioMedicine

Deep sequencing reveals specific bacterial signatures in the subgingival microbiota of healthy subjects. – Eri Ikeda – Clinical Oral Investigations

Close social relationships correlate with human gut microbiota composition. – Kimberly A. Dill-McFarland – Scientific Reports

The gut microbiota heterogeneity and assembly changes associated with the IBD. – Yang Sun – Scientific Reports

The respiratory microbiota: new insights into pulmonary tuberculosis. – Setegn Eshetie – BMC Infectious Diseases

 

Faecal Transplants

Letter to the Editor: Faecal microbiota transplant for eradication of multidrug-resistant Enterobacteriaceae: a lesson in applying best practice? – Benjamin H. Mullish – Clinical Microbiology and Infection

Clinical characteristic and fecal microbiota responses to probiotic or antidepressant in patients with diarrhea-predominant irritable bowel syndrome with depression comorbidity: a pilot study. – Lu Zhang – Chinese Medical Journal

Multi-session fecal microbiota transplantation using colonoscopy has favorable outcomes for the treatment of steroid-dependent ulcerative colitis. – Young-Seok Cho – Intestinal Research

 

Beneficial Microbes and Compounds

Effect of Probiotic Use on Adverse Events in Adult Patients with Inflammatory Bowel Disease: a Retrospective Cohort Study. – Maria Pina Dore – Probiotics and Antimicrobial Proteins

Identification of the novel role of butyrate as AhR ligand in human intestinal epithelial cells. – Ludovica Marinelli – Scientific Reports

Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b metabolic interaction based on 2′-O-fucosyl-lactose studied in steady-state cultures in a Freter-style chemostat. – Manuela Centanni – Applied and Environmental Microbiology

Oral supplements of combined fructo- and xylo-oligosaccharides during perinatal period significantly offsets acrylamide-induced oxidative impairments and neurotoxicity in rats. – Muralidhara Krishna – Journal Of Physiology And Pharmacology

Impact of Grain Sorghum Polyphenols on Microbiota of Normal Weight and Overweight/Obese Subjects during In Vitro Fecal Fermentation. – Danielle Ashley – Nutrients

Geographical location specific composition of cultured microbiota and Lactobacillus occurrence in human breast milk in China. – Mengfan Ding – Food & Function

 

Animal Microbiome

Review: The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States. – Sarah Moraïs – Trends in Microbiology

Gut microbiota affects development and olfactory behavior in Drosophila melanogaster. – Huili Qiao – Journal of Experimental Biology

Genomic diversity landscape of the honey bee gut microbiota. – Kirsten M. Ellegaard – Nature Communications

Abnormal composition of gut microbiota contributes to delirium-like behaviors after abdominal surgery in mice. – Jie Zhang – Neuroscience and Therapeutics

Functional Interactions between Gut Microbiota Transplantation, Quercetin and High Fat Diet Determine Non-Alcoholic Fatty Liver Disease Development in Germ-Free Mice. – David Porras – Molecular Nutrition and Food Research

Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. – Giulia Alessandri – Environmental Microbiology

 

Environmental Microbiome

Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams. – Silas H.W.Vick – iScience

 

Food Microbiome

Book Chapter: Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health. – Laura Lavefve – Advances in Food and Nutrition Research

 

Methodologies

Review: A crash course in sequencing for a microbiologist. – Aleksandra Kozińska – Journal of Applied Genetics

Review: The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies. – Pavan K. Mantravadi – Antibiotics

Effects of the long-term storage of human fecal microbiota samples collected in RNAlater. – Julien Tap – Scientific Reports

A sensitive GC/MS detection method for analyzing microbial metabolites short chain fatty acids in fecal and serum samples. – Shuming Zhang – Talanta

January 23, 2019

Today’s digest is about the distinct microbial networks within disturbed gut microbiome, multifaceted roles of Staphylococcus epidermidis in skin physiology, and high-throughput cultivation techniques. Happy reading!

Urinary microbiome

Review: The Microbiome and Genitourinary Cancer: A Collaborative Review – Mark C. Markowski – European Urology

Gut microbiome

*Microbial network disturbances in relapsing refractory Crohn’s disease – Bahtiyar Yilmaz – Nature Medicine

Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma – Qisha Liu – Gut Pathogens

Human gut microbes are susceptible to antimicrobial food additives in vitro – Lucia Hrncirova – Folia Microbiologica

Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health – Nilusha Malmuthuge – Applied and Environmental Microbiology

Skin microbiome

*Microbial guardians of skin health – Apollo Stacy and Yasmine Belkaid – Science

Water microbiome

Comparison of microbial communities in the sediments and water columns of frozen cryoconite holes in the McMurdo Dry Valleys, Antarctica – Pacifica Sommers – Frontiers in Microbiology

Plant/root/soil microbiome

Invasive plant species identity affects soil microbial communities in a mesocosm experiment – Anna M. Stefanowicz – Applied Soil Ecology

Techniques

*High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria – Dennis Versluis – PlosOne

*Cultivation-success of rare soil bacteria is not influenced by incubation time and growth medium – Viola Kurm – PlosOne

January 15, 2019

Highlights today include the organisms in the healthy infant intestinal microbiome that protect against food allergy, an algorithm to predict aging based on the gut microbiome, and how bacteria adapt to life on the International Space Station. Enjoy!

Pregnancy and early life
Healthy infants harbor intestinal bacteria that protect against food allergy – Taylor Feehley – Nature Medicine

Human gut microbiome
Preprint: Human microbiome aging clocks based on deep learning and tandem of permutation feature importance and accumulated local effects – Fedor Galkin – bioRxiv
(Covered in popular press as Your Gut Microbiome Could Actually Reveal Your Age, Study Shows)

Preprint: The virome in adult monozygotic twins with concordant or discordant gut microbiomes – J. Leonardo Moreno-Gallego – bioRxiv

Human nearly-sterile sites
Review: Microbiome–metabolome reveals the contribution of gut–kidney axis on kidney disease – Yuan-Yuan Chen – Journal of Translational Medicine

Animal experiments
Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo-Min Jang – Molecular Nutrition and Food Research

Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats – Yun Xia – Applied Microbiology and Biotechnology

Impact of intramammary inoculation of inactivated Lactobacillus rhamnosus and antibiotics on the milk microbiota of water buffalo with subclinical mastitis – Carlotta Catozzi – PLOS One

Plant, root, and soil microbiome
Superior dispersal ability can lead to persistent ecological dominance throughout succession – Primrose J. Boynton – Applied and Environmental Microbiology

Plant growth-promoting rhizobacterium Pseudomonas PS01 induces salt tolerance in Arabidopsis thaliana – Thanh Nguyen Chu – BMC Research Notes

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ\

Antifungal potential of bacterial rhizosphere isolates associated with three ethno-medicinal plants (poppy, chamomile, and nettle) – Marija Mojicevic – International Microbiology

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions – Taotao Zeng – Environmental Science and Pollution Research

Water and extremophile microbiomes
An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community – Po-Hsiang Wang – The ISME Journal

Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients – Zhiyuan Yao – Applied and Environmental Microbiology

Effects of salinity on microbialite-associated production in Great Salt Lake, Utah – Melody R. Lindsay – Ecology

Preprint: Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria – Xiaoqin Wu – bioRxiv

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria – Maxim Rubin-Blum – mSphere

Techniques
Generation of 13C-labeled MUC5AC mucin oligosaccharides for stable isotope probing of host-associated microbial communities – Clayton Evert – ACS Infectious Diseases

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism – Hiroki Nishiguchi – Metabolic Engineering

Built environment/Microbes in Space
Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil – Ryan A. Blaustein – mSystems
(Covered in the popular press as Good news: space bacteria (probably) aren’t evolving to destroy us)

Science, publishing, and career
Preprint: Tracking the popularity and outcomes of all bioRxiv preprints – Richard J. Abdill – bioRxiv

January 14, 2019

Human/General Microbiome

Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes – Richard G. Brown – Translational Research

Sex differences in the gut microbiota as potential determinants of gender predisposition to disease – Jose A. Santos‐Marcos – Molecular Nutrition and Food Research

AllergoOncology: microbiota in allergy and cancer – an EAACI position paper – E Untersmayr – Allergy

Comment: Gut microbiota and hypertension – Jun-ichi Oyama – Hypertension Research

Comment: Host-microbiota interactions: from holobiont theory to analysis – Jean-Christophe Simon – Microbiome

Longitudinal Analyses of Gut-Associated Bacterial Microbiota in Ulcerative Colitis Patients – Luma Al-Bayati – Archives of Iranian Medicine

What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases – Emanuele Rinninella – Microorganisms

A Prospective Study In Severely Injured Patients Reveals An Altered Gut Microbiome Is Associated With Transfusion Volume – Susannah E. Nicholson – Journal of Trauma and Acute Care Surgery

Review: Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms – Tsuyoshi Hamada – The Journal of Pathology

Review: Targeting gut microbiota with dietary components on cancer: Effects and potential mechanisms of action – Jun Tao – Critical Reviews in Food Science and Nutrition

Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study – Li Shao – Frontiers in Microbiology

Review: Leveraging Multilayered “Omics” Data for Atopic Dermatitis: A Road Map to Precision Medicine – Debajyoti Ghosh – Frontiers in Immunology

Systemic instruction of cell-mediated immunity by the intestinal microbiome – John Grainger – F1000Research

Fecal microbiota transplantation in refractory ulcerative colitis – a case report – B. D. Moutinho – Journal of International Medical Research

Current Opinion: Acne, the Skin Microbiome, and Antibiotic Treatment – Haoxiang Xu – American Journal of Clinical Dermatology

Fusobacterium nucleatum promotes chemoresistance to 5-fluorouracil by upregulation of BIRC3 expression in colorectal cancer – Sheng Zhang – Journal of Experimental & Clinical Cancer Research

Enteric dysbiosis and fecal calprotectin expression in premature infants – Thao T. B. Ho – Pediatric Research

 

Animal Models

Obesity Aggravates Acute Pancreatitis via Damaging Intestinal Mucosal Barrier and Changing Microbiota Composition in Rats – Cheng Ye – Scientific Reports

Asperlin Stimulates Energy Expenditure and Modulates Gut Microbiota in HFD-Fed Mice – Chongming Wu – Marine Drugs

Preventive Effect of Spontaneous Physical Activity on the Gut-Adipose Tissue in a Mouse Model That Mimics Crohn’s Disease Susceptibility – Florie Maillard – Cells

Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo‐Min Jang – Molecular Nutrition and Food Research

The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome – Heidi H. Pak – Scientific Reports

 

More Animal Microbiomes

Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae (sensu lato) during colonization in the laboratory – Jewelna Akorli – Parasites & Vectors

Potential role of host-derived quorum quenching in modulating bacterial colonization in the moon jellyfish Aurelia aurita – Nancy Weiland-Bräuer – Scientific Reports

 

Beneficial Microbes and Compounds

Review: Effect of Food Structure and Processing on (Poly)phenol-Gut Microbiota Interactions and the Effects on Human Health – Francisco A. Tomás-Barberán – Annual Reviews of Food Science and Technology

Dietary Fructooligosaccharide and Glucomannan Alter Gut Microbiota and Improve Bone Metabolism in Senescence-Accelerated Mouse – Kenichi Tanabe – Journal of Agricultural and Food Chemistry

 

Plant Microbiome

Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome – Joy Bergelson – Scientific Reports

 

January 11, 2019

General Microbiome

A great-ape view of the gut microbiome.Nishida AH. Nature Reviews Genetics

Relative reduction of biological and phylogenetic diversity of the oral microbiota of diabetes and pre-diabetes patients. Saeb ATM. Microbial Pathogenesis

Dietary modulation of the microbiome as therapy.Bernard NJ. Nature Reviews Rheumatology

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.Pacheco AR. Nature Communications

Low-moisture food matrices as probiotic carriers. Marcial-Coba MS . FEMS Microbiology Letters

REVIEW: Cross-Domain and Viral Interactions in the Microbiome.Rowan-Nash AD. Microbiology and Molecular Biology Reviews

The respiratory microbiome and susceptibility to influenza virus infection. Lee KH. PLoS One

Food Microbiome

Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.Marino M. Food Microbiology

Gut Microbiome

Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway.Singh R. Nature Communications

Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms.Sanctuary MR. PLoS One

Nonsteroidal Anti-inflammatory Drugs Alter the Microbiota and Exacerbate <i>Clostridium difficile</i> Colitis while Dysregulating the Inflammatory Response.Maseda D. mBio

Techniques/Resources

OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes. Yadav D. DNA Research

Streamlining standard bacteriophage methods for higher throughput.Kauffman KM. MethodsX

Indirect DNA extraction method suitable for acidic soil with high clay content. Högfors-Rönnholm E. MethodsX

DATABASE: The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection.Rigden DJ. Nucleic Acid Research

Animal Experiments and Microbiome

Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development.Treichel NS. Microbial Ecology

Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis.Miranda-CasoLuengo R. PLoS One.

Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica.Ramírez-Fernández L. PLoS One

Use of 16S rRNA gene sequencing for prediction of new opportunistic pathogens in chicken ileal and cecal microbiota.Kollarcikova M. Poultry Science

Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.Delgado B. Scientific  Reports

 

Marine and Inland Waters

Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.de Sousa AGG. Microbial Ecology

Stratification, nitrogen fixation, and cyanobacterial bloom stage regulate the planktonic food web structure.Loick-Wilde N. Global Change Biology

Analysis of viral and bacterial communities in groundwater associated with contaminated land.Costeira R. Science of the Total Environment

Plant, Soil, and Air Microbiome

The known and the unknown in soil microbial ecology. Baldrian P. FEMS Microbiology Ecology.

Genomic analysis of bacteria in the Acute Oak Decline pathobiome.Doonan J. Microbial Genomics.

Glutathione S-Transferase Enzymes in Plant-Pathogen Interactions.Gullner G. Frontiers in Plant Science

A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.  Cota-Ruiz K. Environmental International

Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California. Ottesen A. Food Microbiology

Temporal Dynamics of Bacterial Communities in Soil and Leachate Water After Swine Manure Application.Rieke EL. Frontiers of Microbiology

January 4, 2019

Highlights of today’s Digest include: animal microbiomes from snakes to bald eagles to porcupines, studies of bacteria promoting plant growth, and a nice review of ‘omics in fermented foods. Happy reading!

Human oral microbiome
Microcosm biofilms cultured from different oral niches in periodontitis patients – Fabian Cieplik – Journal of Oral Microbiology

Xylitol and sorbitol effects on the microbiome of saliva and plaque – Reisha Rafeek – Journal of Oral Microbiology

Human vaginal microbiome
Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis – Hui-Mei Chen – BMC Genomics

Human gut microbiome
Five years of fecal microbiota transplantation – an update of the Israeli experience – Sharon A Greenberg – World Journal of Gastroenterology

Review: Association between the intestinal microbiota and allergic sensitization, eczema, and asthma: A systematic review – Petra Zimmermann – Journal of Allergy and Clinical Immunology

Interplay between food and gut microbiota in health and disease – Niels Banhos Danneskiold-Samsøe – Food Research International

Gut microbiome changes in overweight male adults following bowel preparation – Hui-Mei Chen – BMC Genomics

Animal Microbiome
Preprint: Bacterial Diversity in Feces of Wild Bald Eagles, Turkey Vultures and Common Ravens from the Pacific Northwest Coast, U.S.A. – Rocio Crespo – bioRxiv

Next-generation sequencing analysis reveals high bacterial diversity in wild venomous and non-venomous snakes from India – Sajesh Puthenpurackal Krishnankutty – Journal of Venomous Animals and Toxins including Tropical Diseases

Understanding the roles of surface proteins in regulation of Lactobacillus pentosus HC-2 to immune response and bacterial diversity in midgut of Litopenaeus vannamei – Yang Du – Fish & Shellfish Immunology

Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics – Mackenzie Thornbury – PLOS One

Plant, root, and soil microbiome
Review: Planting the Microbiome – Jennifer K. Spinler – Trends in Microbiology

Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins – Johannes Thürich – PLOS One

Screening of plant growth promotion ability among bacteria isolated from field-grown sorghum under different managements in Brazilian drylands – Jéssica Fernanda da Silva – World Journal of Microbiology and Biotechnology

Streptomyces: implications and interactions in plant growth promotion – Oluwaseyi Samuel Olanrewaju – Applied Microbiology and Biotechnology

Mycorrhizal features and leaf traits covary at the community level during primary succession – J. Rasmus P. Jespersen – Fungal Ecology

Microbial communities controlling methane and nutrient cycling in leach field soils – Cristina P.Fernandez-Baca – Water Research

Gradients of three coastal environments off the South China Sea and their impacts on the dynamics of heterotrophic microbial communities – Xianhua Liu – Science of the Total Environment

New insights into the impact of nZVI on soil microbial biodiversity and functionality – Carmen Fajardo – Journal of Environmental Science and Health, Part A

Syntrophic effect of indigenous and inoculated microorganisms in the leaching of rare earth elements from Western Australian monazite – Melissa K.Corbett – Research in Microbiology

Removal of veterinary antibiotics in constructed wetland microcosms – Response of bacterial communities – Filipa Santos – Ecotoxicology and Environmental Safety

Water and extremophile microbiome
Bacterial diversity in the water column of meromictic Lake Cadagno and evidence for seasonal dynamics – Francesco Danza – PLOS One

Microbial community succession and pollutants removal of a novel carriers enhanced duckweed treatment system for rural wastewater in Dianchi Lake basin – Guoke Chen – Bioresource Technology

Food Microbiology
Omics in traditional vegetable fermented foods and beverages – Jocelin Rizo – Critical Reviews in Food Science and Nutrition

Preprint: Construction of synthetic microbiota for reproducible flavor metabolism in Chinese light aroma type liquor produced by solid-state fermentation – Qun Wu – bioRxiv

Bioinformatics
A latent allocation model for the analysis of microbial composition and disease – Ko Abe – BMC Bioinformatics

Techniques
Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome – Matthew J. Scarborough – mSystems