June 11, 2019

Today’s digest is about microbiome and Alzheimer’s disease association, global survey of arsenic related genes in soil microbiome,  Bifidobacterium bifidus in infant gut and a preprint on selection in host microbiome evolution.

General microbiome

Understanding the Role of the Gut Microbiome and Microbial Metabolites in Obesity and Obesity-Associated Metabolic Disorders: Current Evidence and Perspectives – Natalia Vallianou – Current Obesity Reports

Alzheimer’s disease and symbiotic microbiota: an evolutionary medicine perspective – Molly Fox – Annals of the New York Academy of Sciences

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis – Jessica L. Mark Welch – Annual Review of Microbiology

Human microbiome

Colonic mucosal and exfoliome transcriptomic profiling and fecal microbiome response to a flaxseed lignan extract intervention in humans – Johanna W. Lampe – American journal of Clinical Nutrition

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals – Riccardo Vasapolli – Gastroenterology

Identification of Salivary Microbiota and its Association with Host Inflammatory Mediators in Periodontitis – Anna Lundmark – Frontiers in Cellular and Infection Microbiology

Effect of the Degree of Polymerization of Fructans on Ex Vivo Fermented Human Gut Microbiome – Erola Astó – Nutrients

Inflammatory skin is associated with changes in the skin microbiota composition on the back of severe acne patients – Marie-Ange Dagnelie – Experimental Dermatology

Gut microbiota development of preterm infants hospitalised in intensive care units – H. Tauchi – Beneficial Microbes

Animal experiments

Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota – Devin B. Holman – Microbiome

Sequential changes in the host gut microbiota during infection with the intestinal parasitic nematode Strongyloides venezuelensis – Tanzila Afrin – Frontiers in Cellular and Infection Microbiology

Plant, root, soil microbiome

A global survey of arsenic-related genes in soil microbiomes – Taylor K. Dunivin – BMC Biology

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics – Nengfei Wang – Microbes and Environments

Water microbiome and extremophiles

Comparison of the microbiomes of two drinking water distribution systems—with and without residual chloramine disinfection – Michael B. Waak – Microbiome

Probiotics

Probiotics may not prevent the deterioration of necrotizing enterocolitis from stage I to II/III – Zheng-Li Wang – BMC Pediatrics

Bifidobacterium bifidum and the infant gut microbiota: an intriguing case of microbe‐host co‐evolution – Sabrina Duranti – Environmental Microbiology

Techniques

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes – G.A.Arango-Argoty – Microbiome

Metabolic route computation in organism communities – Markus Krummenacker – Microbiome

The role of multilevel selection in host microbiome evolution – Simon van Vliet – BioRxiv

Microbes and the market

Human Microbiome Therapeutics Market Analysis 2019: With Top 20 Countries data, Product Types, Segmentation, Market Share Analysis, Influential Trends And Challenges, Forecast To 2023 – Saginaw Daily

Global Human Microbiome Based Drugs and Diagnostics Market Potential Growth 2019 | Second Genome Inc., Enterome Bioscience, Yakult – Business Tech Hub

Human Microbiome Market 2024 Significant Development | Future Trends of Key Players by Size and Share – The Warren Daily

In-Depth Research Report of Global Microbiome Sequencing Services Market (2019 Version), with Types, Application, and Manufactures – the Pueblo Daily

Microbiome Sequencing Services Market Key Players, Industry Overview, Demand & Supply Chain Analysis, Forecast To 2024 – Burbank Observer

Human Microbiome Market Growth, Trend and Forecast 2018-2026 – Business Herald

 

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June 4, 2019

General microbiome
Rigorous Statistical Methods for Rigorous Microbiome Science – Amy D. Willis – mSystems

Understanding microbial community dynamics to improve optimal microbiome selection – Robyn J. Wright – Microbiome

Toward a Better Understanding of Species Interactions through Network Biology – Ryan S. McClure – mSystems

Human respiratory microbiome
Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus – Hyun Jik Kim – Microbiome

Human gut microbiome
A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans – Alfonso Benítez-Páez – mSystems

Gut microbiome identifies risk for colorectal polyps – Ezzat Dadkhah – BMJ Open Gastroenterology

Yogurt improves insulin resistance and liver fat in obese women with nonalcoholic fatty liver disease and metabolic syndrome: a randomized controlled trial – Yang Chen – American Journal of Clinical Nutrition

Preprint: Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids – Robert A Quinn – bioRxiv

Animal models
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model – Limei Lin – Microbiome

Missing Links: the Role of Primates in Understanding the Human Microbiome – Katherine R. Amato – mSystems

Plant, root, and soil microbiome
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays – Frank Reith – Annals of Botany

Water and extremophile microbiome
Effects of sulfamethoxazole and sulfamethoxazole-degrading bacteria on water quality and microbial communities in milkfish ponds – Bea-Ven Chang – Environmental Pollution

Preprint: Temporal dynamics of Bacteria, Archaea and protists in equatorial coastal waters – Caroline Chénard – bioRxiv

Built environment
Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area – Miles Richardson – Microbiome

Phages and viruses
Preprint: The human gut virome is highly diverse, stable and individual-specific – Andrey Shkoporov – bioRxiv

Bioinformatics
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language – Luis Pedro Coelho – Microbiome

Science, publishing, and career
Preprint: The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Rochelle E. Tractenberg – bioRxiv

Alyson’s non-microbiology picks
Why Your Metro Commute Is So Insanely Windy – Julie Bogen – The Atlantic

The 2019 Wellcome photography prize: close focus on the human condition – Sean O’Hagan – The Guardian

May 21, 2019

Today’s digest is short and sweet but includes interesting articles. A brilliant essay on multidisciplinarity in microbiome research 🥰

General Microbiome

ESSAY: Multidisciplinarity in Microbiome Research: A Challenge and Opportunity to Rethink Causation, Variability, and Scale. KR Amato – BioEssays

REVIEW:Contribution of the Mucosal Microbiota to Bovine Respiratory HealthM Zeineldin. Trends in Microbiology

Characterization of a novel salt-, xylose-and alkali-tolerant GH43 bifunctional β-xylosidase/α-l-arabinofuranosidase from the gut bacterial genome. B Xu. Journal of Bioscience and Bioengineering

Gut Microbiome

Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular CarcinomaEJ Cho. Scientific Reports

The bacterial communities of the small intestine and stool in children with short bowel syndrome. SL Zeichner. PLOS ONE

Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approachesGA Lugli. BMC Genome Biology

Plant, Soil, and Water Microbiome

Microbial production and consumption of dissolved organic matter in glacial ecosystems on the Tibetan PlateauL Zhou. Water Research

Engineering banana endosphere microbiome to improve Fusarium wilt resistance in banana. Y Liu.Microbiome
Toxic responses of metabolites, organelles and gut microorganisms of Eisenia fetida in a soil with chromium contaminationR Tang. Environmental Pollution

Roles of microbes in supporting sustainable rice production using the system of rice intensificationF Doni. Applied Microbiology and Biotechnology

Cover crop species have contrasting influence upon soil structural genesis and microbial community phenotype.A Bacq-Labreuil. Scientific Reports

Preprint

Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn’s Disease Cohort . Daniel Sprockett. bioRxiv posted 19 May 2019

May 20, 2019

This Monday, read about the stability within gut resident clonal populations of Enterobacteriaceae, significance of microbiome in personalized medicine, and impacts of intermittent supply on the drinking water microbiome. Happy reading!

General microbiome

Defining Microbiome Health through a Host Lens – Sean M. Gibbonsa – mSystems

*Review: The significance of microbiome in personalized medicine – Ava Behrouzi – Clinical and Translational Medicine

Moving towards a Robust Definition for a “Healthy” Indoor Microbiome – Karen C. Dannemiller – mSystems

Gut microbiome

*Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults – Jonathan N. V. Martinson – ISME Journal

Rectal swabs in critically-ill patients provide discordant representations of the gut microbiome compared to stool samples: a brief methodologic report – Katherine Fair – bioRxiv

Development of a Covalent Inhibitor of Gut Bacterial Bile Salt Hydrolases – Arijit A. Adhikari – bioRxiv

Temporal Gut Microbial Changes Predict Recurrent Clostridium difficile in Patients with and without Ulcerative Colitis – Allen A. Lee – boRxiv

Alteration of Gut Microbiome in Lung Cancer Patients – Li Ming – bioRxiv

Respiratory microbiome

Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in humans and ferrets – Drishti Kaul – bioRxiv

High mortality from viral pneumonia in patients with cancer – Youn-Jung Ki – Infectious Diseases

Water microbiome

Global diversity and biogeography of bacterial communities in wastewater treatment plants – Linwei Wu – Nature Microbiology

*Understanding the impacts of intermittent supply on the drinking water microbiome – Quyen Melina Bautista-de los Santos – Current Opinion in Biotechnology

Animal microbiome

Exploration of the rumen microbial diversity and carbohydrate active enzyme profile of black Bengal goat using metagenomic approach – Prashant R. Suryawanshi – Animal Biotechnology

Assessing key microbial communities determining nitrogen transformation in composting of cow manure using illumina high-throughput sequencing – Yu Sun – Waste Management

Plant/root/soil microbiome

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations – Thorsten Thiergart – bioRxiv

Response of Microbial Communities and Their Metabolic Functions to Drying–Rewetting Stress in a Temperate Forest Soil – Dong Liu – Microorganisms

Review: Rhizosphere size and shape: Temporal dynamics and spatial stationarity – Yakov Kuzyakov & Bahar S. Razavi – Soil Biology and Biochemistry

Phages and viruses

Production and characterization of novel ssRNA bacteriophage virus-like particles from metagenomic sequencing data – Ilva Lieknina – Journal of Nanobiotechnology

Techniques

PhenoGMM: Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity – Peter Rubbens – bioRxiv

April 28, 2019

Human Gut and General Microbiome

Review: Stereotypes About Enterotype: the Old and New Ideas – Mingyue Cheng – Genomics, Proteomics & Bioinformatics

Review: Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity – Eric M. Brown –  Annual Review of Immunology

Review: The Microbiome and Food Allergy – Onyinye I. Iweala – Annual Review of Immunology

Review: An Updated Review of Clostridium difficile Treatment in Pediatrics – Christopher T. Campbel –  The Journal of Pediatric Pharmacology and Therapeutics

Review: Pediatric inflammatory bowel disease: continuous lessons for adult inflammatory bowel disease – Shahzad Ahmed – Current Opinion in Gastroenterology

Review: Intestinal Microbiota in Cardiovascular Health and Disease: JACC State-of-the-Art Review – W.H. Wilson Tang – Journal of the American College of Cardiology

Review: The role of the gut microbiome in sex differences in arterial pressure – Anna L. Beale – Biology of Sex Differences

Review: Precision Nutrition and the Microbiome, Part I: Current State of the Science – Susan Mills – Nutrients

Review: Impact of bariatric surgery on type 2 diabetes: contribution of inflammation and gut microbiome? – Jean Debédat – Seminars in Immunopathology

Review: The Gut Microbiota-Host Partnership as a Potential Driver of Kawasaki Syndrome – Susanna Esposito – Frontiers in Pediatrics

Review: A Review of Mixed Strain Clostridium difficile Colonization and Infection – Pete Dayananda – Frontiers in Microbiology

Review: Small Intestinal Bacterial Overgrowth in Patients With Cirrhosis – Gaurav Ghosh – Journal of Clinical and Experimental Hepatology

Perspective: Effect of Metformin on Antipsychotic-Induced Metabolic Dysfunction: The Potential Role of Gut-Brain Axis – Chao Luo –  Frontiers in Pharmacology

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome – Jun Li – Genomics, Proteomics & Bioinformatics

Contribution of Non-immune Cells to Activation and Modulation of the Intestinal Inflammation – Renata Curciarello – Frontiers in Immunology

Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan – Yukuto Sato – Scientific Reports

The short-chain fatty acid propionate increases glucagon and FABP4 production, impairing insulin action in mice and humans – Amir Tirosh – Science Translational Medicine

 

Cancer and Microbiome

The diversity of gut microbiome is associated with favorable responses to anti-PD-1 immunotherapy in Chinese non-small cell lung cancer patients – Yueping Jin – Journal of Thoracic Oncology

Gut Microbiota as a Positive Potential Therapeutic Factor in Carcinogenesis: an Overview of Microbiota-Targeted Therapy – Farahnaz Joukar – Journal of Gastrointestinal Cancer

Detection of Fusobacterium nucleatum in stool and colonic tissues from Norwegian colorectal cancer patients – Hege Smith Tunsjø – European Journal of Clinical Microbiology & Infectious Diseases

 

Oral Microbiome

Gender-Specific Associations Between Saliva Microbiota and Body Size  – Sajan C. Raju – Frontiers in Microbiology

Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis – Bo-Young Hong – Microbiome

 

Respiratory Tract Microbiome

The airway microbiota in children newly diagnosed with bronchiectasis largely retains its diversity – Naveen Pillarisetti – European Respiratory Journal

Performance of the Biomark HD real-time qPCR System (Fluidigm) for the detection of nasopharyngeal bacterial pathogens and Streptococcus pneumoniae typing – Courtney P. Olwagen – Scientific Reports

 

Mother and Child Microbiome

Systematic Review: Repertoire of human breast and milk microbiota: a systematic review – Amadou Togo – Future Medicine

Variation of cultured skin microbiota in mothers and their infants during the first year postpartum – Georgios Gaitanis – Pediatric Dermatology

 

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment – Ning Li – Genomics, Proteomics & Bioinformatics

 

Reproductive tract Microbiome

Impact of reproductive aging on the vaginal microbiome and soluble immune mediators in women living with and at-risk for HIV infection – Kerry Murphy – PLoS ONE

The Vaginal and Urinary Microbiomes in Premenopausal Women With Interstitial Cystitis/Bladder Pain Syndrome as Compared to Unaffected Controls: A Pilot Cross-Sectional Study – Kate V. Meriwether – Frontiers in Cellular and Infection Microbiology

Microorganisms in the healthy upper reproductive tract: from denial to beneficial assignments for reproductive biology – Rebekka Einenkel – Reproductive Biology

 

Animal Microbiome

Structural shifts in the intestinal microbiota of rats treated with cyclosporine A after orthotropic liver transplantation – Junjun Jia – Frontiers of Medicine

Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax) – Wen Wang – International Microbiology

Antibiotics-induced perturbations in gut microbial diversity influence metabolic phenotypes in a murine model of high-fat diet-induced obesity – Dongmin Liu – Applied Microbiology and Biotechnology

Rumen fermentation, intramuscular fat fatty acid profiles and related rumen bacterial populations of Holstein bulls fed diets with different energy levels – Haibo Wang – Applied Microbiology and Biotechnology

The Gut Microbiome on a Periodized Low-Protein Diet Is Associated With Improved Metabolic Health – Zhencheng Li – Frontiers in Microbiology

Human activity can influence the gut microbiota of Darwin’s finches in the Galapagos Islands – Sarah A. Knutie – Molecular Ecology

Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters – Colin Fogarty – Journal of Applied Microbiology

Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea – Haiyan Xu – Food & Nutrition

Microbiome analysis of Ixodes scapularis ticks from New York and Connecticut – Rafal Tokarz – Ticks and Tick-borne Diseases

Human gut microbiota transferred to germ-free NOD mice modulate the progression towards type 1 diabetes regardless of the pace of beta cell function loss in the donor – Vit Neuman – Diabetologia

Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors – Barbora Pafčo – American Journal of Physical Anthropology

The bumble bee microbiome increases survival of bees exposed to selenate toxicity – Jason A. Rothman – Environmental Microbiology

Effect of probiotic supplementation on seizure activity and cognitive performance in PTZ-induced chemical kindling – Samaneh Bagheri – Epilepsy and Behavior

Inulin Can Alleviate Metabolism Disorders in ob/ob Mice by Partially Restoring Leptin-Related Pathways Mediated by Gut Microbiota – Xiaofeng Song – Genomics, Proteomics & Bioinformatics

Supplementation with compound polysaccharides contributes to the development and metabolic activity of young rat intestinal microbiota – Mengxia Wang – Food & Nutrition

A Risky Business? Habitat and Social Behavior Impact Skin and Gut Microbiomes in Caribbean Cleaning Gobies – Raquel Xavier – Frontiers in Microbiology

Ovarian progesterone suppresses depression and anxiety-like behaviors by increasing the Lactobacillus population of gut microbiota in ovariectomized mice – Watcharin N.Sovijit – Neuroscience Research

 

Beneficial Microbes and Compounds

Meta-analysis: Probiotics improve glucose and lipid metabolism in pregnant women: a meta-analysis – Man-Man Han – Annals of Translational Medicine

Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis – Jiachao Zhang – mSystem

Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts – Guangwen Luo – Frontiers in Microbiology

The beneficial effects of purple yam (Dioscorea alata L.) resistant starch on hyperlipidemia in high-fat-fed hamsters – Tao Li – Food & Nutrition

Restoration of Bacterial Microbiome Composition and Diversity Among Treatment Responders in a Phase 2 Trial of RBX2660: An Investigational Microbiome Restoration Therapeutic – Ken F Blount – Open Forum Infectious Diseases

Lactobacillus reuteri DSM 17938 – A comparative study on the effect of probiotics and lysates on human skin – I. Khmaladze – Experimental Dermatology

 

Plant and Soil Microbiome

Nodulation induces systemic resistance of Medicago truncatula and Pisum sativum against Erysiphe pisi and primes for powdery mildew-triggered salicylic acid accumulation – Lara Smigielski – IS-MPMI

Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest – Gileno V. Lacerda-Júnior – Frontiers in Microbiology

Microbial Diversity in the Edible Gall on White Bamboo Formed by the Interaction between Ustilago esculenta and Zizania latifolia – Zhihao Tu – Current Microbiology

Species-specific response of the soil collembolan gut microbiome and resistome to soil oxytetracycline pollution – Qi Zhang – Science of The Total Environment

 

Food Microbiome

Gamma Irradiation Influences the Survival and Regrowth of Antibiotic-Resistant Bacteria and Antibiotic-Resistance Genes on Romaine Lettuce – Vaishali Dharmarha – Frontiers in Microbiology

 

Bioinformatics

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes – Xiaoqing Jiang – Genomics, Proteomics & Bioinformatics

Phy-PMRFI: Phylogeny-aware Prediction of Metagenomic Functions using Random Forest Feature Importance – Jyotsna Talreja Wassan – IEEE Transactions on NanoBioscience

 

Other

Flood Season Microbiota from the Amazon Basin Lakes: Analysis with Metagenome Sequencing – Célio Dias Santos Júnior – Microbiology Resource Announcements

Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium – Mathew P. Watts – Water Research

8 April, 2019

General Microbiome

Coevolutionary dynamics shape the structure of bacteria-phage infection networks. Fortuna MA.Evolution.

High proportions of bacteria are culturable across major biomes. Martiny AC. ISME Journal

The complexity of an optimal vaginal biome. Eschenbach DA. BJOG

The lung microbiome, vitamin D, and the tuberculous granuloma: A balance triangle. Balcells ME. Microbial Pathogenesis

Gut Microbiome

The parasitic worm product ES-62 normalises the gut microbiota bone marrow axis in inflammatory arthritis. Doonan J. Nature Communications

Culture-enriched human gut microbiomes reveal core and accessory resistance genes. Raymond F.Microbiome.

Plant, Soil, Water, and Air Microbiome

Temperature and soil moisture control microbial community composition in an arctic-alpine ecosystem along elevational and micro-topographic gradients.Frindte K. ISME Journal

Root traits and belowground herbivores relate to plant-soil feedback variation among congeners.Wilschut RA. Nature Communications

A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms.Stamou GP. Microbial Ecology

Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota.Deng Y. Applied Microbiology Biotechnology

Rapid and stable microbial community assembly in the headwaters of third-order stream. Teachey ME. Applied Environmental Microbiology

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential After Two Years of Biochar Amendment in a Tropical Oxisol. Yu J. Applied Environmental Microbiology

Animal Experiments and Microbiome

Effect of a low protein diet on chicken ceca microbiome and productive performances. De Cesare A. Poultry Science

Impact of a probiotic-based cleaning product on the microbiological profile of broiler litters and chicken caeca microbiota.De Cesare P. Poultry Science

Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim. Grieco MB. Current Microbiology.

The hemolymph microbiome of insects. Blow F. Journal Of Insect Physiology

Musa basjoo regulates the gut microbiota in mice by rebalancing the abundance of probiotic and pathogen. Wei T. Microbial Pathogenesis

Investigating the influence of organic acid marinades, storage temperature and time on the survival/inactivation interface of Salmonella on chicken breast fillets.

Lytou AE. International Journal of Food Microbiology.

March 21, 2019

Happy Spring! Today’s Digest features a megaphylogeny of mushrooms, new papers about the respiratory microbiome, fecal microbiome and metatranscriptomic analysis from nonhuman primates, and the microbial ecology of snow. Bonus: a pick about the first woman to win the Abel Prize.

General Microbiome
Megaphylogeny resolves global patterns of mushroom evolution – Torda Varga – Nature Ecology and Evolution

Fate of CMY-2-encoding plasmids introduced into the human fecal microbiota by exogenous Escherichia coli – Mehreen Anjum – Antimicrobial Agents and Chemotherapy

Review: The impact of indigenous microbes on Parkinson’s disease – Timothy Sampson – Neurobiology of Disease

Pregnancy and Early Life
Michigan cohorts to determine associations of maternal pre-pregnancy body mass index with pregnancy and infant gastrointestinal microbial communities: Late pregnancy and early infancy – Kameron Y. Sugino – PLOS One

Human Respiratory Microbiome
Bacterial and viral respiratory tract microbiota and host characteristics in children with lower respiratory tract infections: a matched case-control study – Wing Ho Man – The Lancet Respiratory Medicine

The Yin and Yang of Streptococcus Lung Infections in Cystic Fibrosis: A Model for Studying Polymicrobial Interactions – Jessie E. Scott – Journal of Bacteriology

The nasal and oropharyngeal microbiomes of healthy livestock workers – Ashley E. Kates – PLOS One

Human Gut Microbiome
Review: Role of SCFAs in gut microbiome and glycolysis for colorectal cancer therapy – Gang Wang – Journal of Cellular Physiology

Review: Obesity, Motility, Diet, and Intestinal Microbiota—Connecting the Dots – Maya Fayfman – Current Gastroenterology Reports

Review: The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies – Jun Gong – Clinical and Translational Medicine

The exosome secretion inhibitor neticonazole suppresses intestinal dysbacteriosis-induced tumorigenesis of colorectal cancer – Lei Gu – Investigational New Drugs

Glutamate interactions with obesity, insulin resistance, cognition and gut microbiota composition – María Encarnación Palomo-Buitrago – Acta Diabetologica

Understanding the gut–kidney axis among biopsy-proven diabetic nephropathy, type 2 diabetes mellitus and healthy controls: an analysis of the gut microbiota composition – Sibei Tao – Acta Diabetologica

Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rRNA amplicon sequencing – Tadashi Ohara – PLOS One

Animal Experiments
Gut microbiota from infant with Cow’s Milk Allergy promotes clinical and immune features of atopy in a murine model – A. Mauras – Allergy

N-(1-carbamoyl-2-phenylethyl) butyramide reduces antibiotic-induced intestinal injury, innate immune activation and modulates microbiota composition – Adriano Lama – Scientific Reports

Immunosuppression-induced alterations in fish gut microbiota may increase the susceptibility to pathogens – Xiao-Zhou Qi – Fish & Shellfish Immunology

Rifaximin Alters Intestinal Microbiota and Prevents Progression of Ankylosing Spondylitis in Mice – Lianjun Yang – Frontiers in Cellular and Infection Microbiology

Hydroxytyrosol Improves Obesity and Insulin Resistance by Modulating Gut Microbiota in High-Fat Diet-Induced Obese Mice – Zhuoqun Liu – Frontiers in Microbiology

Review: Dietary Fiber and Intestinal Health of Monogastric Animals – Rajesh Jha – Frontiers in Veterinary Science

Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken – Anne-Sophie Charlotte Hieke – PeerJ

Animal Microbiome
Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization – Samuel T. Westreich – Microbiome

Microbiome Profiles of Ligature-Induced Periodontitis in Nonhuman Primates Across the Lifespan – Sreenatha Kirakodu – Infection and Immunity

Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria – Ida Nordang Kieler – Scientific Reports

Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis – Aránzazu Portillo – PLOS One

Plant, Root, and Soil Microbiome
Microbiota in Non-flooded and Flooded Rice Culms – Hui-Ling Cui – FEMS Microbiology Ecology

Microbial community structure in full scale anaerobic mono-and co-digesters treating food waste and animal waste – Taewoan Koo – Bioresource Technology

Variations in pH significantly affect cadmium uptake in grafted muskmelon (Cucumis melo L.) plants and drive the diversity of bacterial communities in a seedling substrate – Jian Zhang – Plant Physiology and Biochemistry

Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation – Martin Taubert – PLOS One

Microbial diversity and soil physiochemical characteristic of higher altitude – Saurabh Kumar – PLOS One

Water and Extremophile Microbiome
Microbial Ecology of Snow Reveals Taxa-Specific Biogeographical Structure – Shawn P. Brown – Microbial Ecology

Bacterial community in cold and alkaline environments of Hoh Xil basin in Qinghai–Tibet Plateau and isolation of potential sources of microbiota – Rui Xing – Annals of Microbiology

Bacterial communities of the microbial mats of Chokrak sulfide springs – Ekaterina I. Burganskaya – Archives of Microbiology

Dynamics of microbial community in the bioreactor for bisphenol S removal – Wen-Cong Huang – Science of the Total Environment

High-throughput DNA sequencing reveals the dominance of pico- and other filamentous cyanobacteria in an urban freshwater Lake – Hanyan Li – Science of the Total Environment

A novel phenol and ammonia recovery process for coal gasification wastewater altering the bacterial community and increasing pollutants removal in anaerobic/anoxic/aerobic system – Xuefei Gui – Science of the Total Environment

Built Environment
Biodeterioration of mortar coating in historical buildings: Microclimatic characterization, material, and fungal community – Fernanda L. Guerra – Building and Environment

A different suite: The assemblage of distinct fungal communities in water-damaged units of a poorly-maintained public housing building – Iman A. Sylvain – PLOS One

Microbes in Space
Subsurface Microbial Habitats in an Extreme Desert Mars-Analog Environment – Kimberley A. Warren-Rhodes – Frontiers in Microbiology

Food Microbiology
Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh – Md Javed Foysal – Journal of Applied Microbiology

Impact of turning, pod storage and fermentation time on microbial ecology and volatile composition of cocoa beans – Yasmine Hamdouche – Food Research International

Probiotic potential of a Lactobacillus rhamnosus cheese isolate and its effect on the fecal microbiota of healthy volunteers – Joaquin Bautista-Gallego – Food Research International

Dynamics of biogenic amines and bacterial communities in a Thai fermented pork product Nham – Pannita Santiyanont – Food Research International

Probiotics/Prebiotics
16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics – Christine Tara Peterson – PLOS One

Phages and Viruses
Review: Phage therapy: What factors shape phage pharmacokinetics and bioavailability? Systematic and critical review – Krystyna Dąbrowska – Medicinal Research Reviews

Bioinformatics
MetaPheno: A Critical Evaluation of Deep Learning and Machine Learning in Metagenome-Based Disease Prediction – Nathan LaPierre – Methods

Assessing alignment-based taxonomic classification of ancient microbial DNA – Raphael Eisenhofer – PeerJ

Techniques
A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss) – Mathis Hildonen – Journal of Microbiological Methods

Alyson’s Non-Microbiology Picks
Soap-bubble pioneer is first woman to win prestigious maths prize

Girls who share a womb with boys tend to make less money than those with twin sisters