April 04, 2019

In today’s microbiome digest, multiple research and review articles focusing on the role of host-associated microbiomes in various diseases including Type 2 Diabetes, Obesity, Urolithiasis, Bronchial Asthma, Cancer Immunotherapy, Hepatic Glycan Storage, Uveitis, Schizophrenia and the Development of the immune system. Enjoy reading.

General microbiome

Harnessing microbiota interactions to produce bioactive metabolites: communication signals and receptor proteins – Juan F Martin – Current Opinion in Pharmacology

Review: Prevention of allergy with diverse and healthy microbiota:an update – Diana Chernikova – Current Opinion in Pediatrics

State of the Art: Pharmacomicrobiomics: The holy grail to variability in drug response? – Anukriti Sharma – Clinical Pharmacology and Therapeutics

Gut microbiome

The alteration of gut microbiota in newly diagnosed type 2 diabetic patients – Pei-Chi Chen – Nutrition

Defining Dysbiosis in Patients with Urolithiasis – Anna Zampini – Scientific Reports

Review: Gut Microbiota, Host Organism, and Diet Trialogue in Diabetes and Obesity – Veronica Lazar – Frontiers in Nutrition

Metabolic activity of intestinal microflora in patients with bronchial asthma – Vladimir Irashkin – Clinics and Practice

Pharmacologic and Nonpharmacologic Therapies for the Gut Microbiota in Type 2 Diabetes – Robert Caesar – Canadian Journal of Diabetes

Review: Modulation of cancer immunotherapy efficacy by gut microbiota – Huo S – Discovery Medicine

Hepatic glycogen storage diseases are associated to microbial dysbiosis – Karina Colonetti – PLOS ONE

Implicating Dysbiosis of the Gut Fungal Microbiome in Uveitis, an Inflammatory Disease of the Eye – Rajagopalaboopathi Jayasudha – Immunology and Microbiology

Cohort profile: The LoewenKIDS Study – life-course perspective on infections, the microbiome and the development of the immune system in early childhood – Cornelia Gottschick – International Journal of Epidemiology

Case Report: Decreased Clostridium Abundance after Electroconvulsive Therapy in the Gut Microbiota of a Patient with Schizophrenia – Misako Kanayama – Case Reports in Psychiatry

Reproductive tract microbiome

Effects of oral probiotic supplements on vaginal microbiota during pregnancy: a randomised, double‐blind, placebo‐controlled trial with microbiome analysis – S Husain – BJOG 

Skin microbiome

Review: The Cutaneous Microbiome: Implications for Dermatology Practice – Megan A. Sander

Animal microbiome / Animal experiments

Intestinal microbiota of broilers submitted to feeding restriction and its relationship to hepatic metabolism and fat mass: Fast-growing strain – Raquel Lunedo – Journal of Animal Physiology and Animal Nutrition

Phytate degradation, intestinal microbiota, microbial metabolites and immune values are changed in growing pigs fed diets with varying calcium–phosphorus concentration and fermentable substrates – Charlotte Maria Elisabeth Heyer – Journal of Animal Physiology and Animal Nutrition

Review: The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs – Lydia K. Greene – American Journal of Primatology

A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome – Asha Jaja-Chimedza – Journal of Functional Foods

Musca domestica Cecropin (Mdc) Alleviates Salmonella typhimurium-Induced Colonic Mucosal Barrier Impairment: Associating With Inflammatory and Oxidative Stress Response, Tight Junction as Well as Intestinal Flora – Lun Zhang – Frontiers in Microbiology

The Effects of Unfermented and Fermented Cow and Sheep Milk on the Gut Microbiota – Elizabeth A. Rettedal – Frontiers in Microbiology

Water and extremophile microbiome

Microbiota of the Hickey Run Tributary of the Anacostia River – Robin Cagle – Microbiology Resource Announcements

Bioinformatics

Review: Statistical Analysis of Metagenomics Data – M. Luz Calle – Genomics and Informatics

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April 1, 2019

In today’s digest read about covert pathogenesis in urinary tract, microbial fuel cells in treatment of organic acid fermentation wastewater, gut microbial metabolism in weanling pigs, and more. Enjoy!

Urinary microbiome

*Covert pathogenesis: Transient exposures to microbes as triggers of disease – Nicole M. Gilbert, Amanda L. Lewis – PlosPathogens

Evaluation of antibacterial efficacy of sulfur nanoparticles alone and in combination with antibiotics against multidrug-resistant uropathogenic bacteria – Priti Paralikar – Journal of Environmental Science and Health, Part A

Review: A Comprehensive Review of Overactive Bladder Pathophysiology: On the Way to Tailored Treatment – Benoit Peyronnet – European Urology

Vaginal microbiome

Effect of progesterone on Candida albicans biofilm formation under acidic conditions: a transcriptomic analysis – Bruna Gonçalves – bioRxiv

Skin microbiome

Cutibacterium acnes antibiotic production shapes niche competition in the human skin microbiome – Jan Claesen – bioRxiv

Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome – Xinzhao Tong – mSystems

Gut Microbiome

The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding – Yu Liu – Frontiers in Microbiology

Gut Microbiome Functional and Taxonomic Diversity within an Amazonian semi-nomadic hunter-gatherer group – Liliane Costa Conteville – bioRxiv

Risk of inflammatory bowel disease after Campylobacter jejuni and Campylobacter concisus infection: a population-based cohort study – Hans Mittle Nielsen – Scandinavian Journal of Gastroenterology

Unilateral ureteral obstruction causes gut microbial dysbiosis and metabolome disorders contributing to tubulointerstitial fibrosis – Lin Chen – Experimental & Molecular Medicine

Oral microbiome

Polymicrobial synergy within oral biofilm promotes invasion of dendritic cells and survival of consortia members – Ahmed El-Awady – Biofilms and Microbiomes

Animal microbiome

*Metagenomic reconstructions of gut microbial metabolism in weanling pigs – Weilan Wang – Microbiome

Probiotics/Prebiotics

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling – Juliana M. Ansari – PlosOne

Biosurfactant Production by Lactic Acid Bacterium Pediococcus dextrinicus SHU1593 Grown on Different Carbon Sources: Strain Screening Followed by Product Characterization – Abouzar Ghasemi – Scientific Reports

Phages and viruses

Bacteriophage adherence to mucus mediates preventive protection against pathogenic bacteria – Gabriel MF Almeida – bioRxiv

Review: The gut virome: the ‘missing link’ between gut bacteria and host immunity? – Indrani Mukhopadhya – Therapeutic Advances in Gastroenterology

Soil microbiome

Shift of the microbial communities from exposed sandstone rocks to forest soils during pedogenesis – Yaping Liu – International Biodeterioration & Biodegradation

Water and extremophile microbiome

Startup, performance, and microbial communities of an anammox reactor inoculated with indigenous sludge for the treatment of high-salinity and mesophilic underground brine – Nobuyuki Yokota – Clean Technologies and Environmental Policy

*Power generation and microbial community analysis in microbial fuel cells: A promising system to treat organic acid fermentation wastewater – Tian Xia – Bioresource Technology

Techniques

Cultivating in situ triggers growth of previously uncultivated microorganisms via a growth initiation factor in nature – Dawoon Jung – bioRxiv

Bioinformatics

Library preparation and sequencing platform introduce bias in metagenomics characterisation of microbial communities – Casper S. Poulse – bioRxiv

March 28, 2019

Today’s digest covers interesting reviews on different aspects of host-microbiome interactions, research articles about how structural variation in gut microbiome affects host health, characterization of a simplified microbial community to study microbial interaction with diet in mice and viral diversity in soil metagenomes. Happy reading!

General microbiome

Review – Microbiome: Our opponents or allies in healthcare and medicine – Horst A von Recum – Experimental Biology and Medicine

Review –  To B12 or not to B12: Five questions on the role of cobalamin in host-microbial interactions – Carol A. Rowley – Plos Pathogens

Review – Can oral bacteria affect the microbiome of the gut? – Ingar Olsen – Journal of Oral Microbiology

Review –  Inter-kingdom signaling between gut microbiota and their host – Qing Li – Cellular and Molecular Life Sciences

Human gut microbiome

Structural variation in the gut microbiome associates with host health – David Zeevi – Nature

Effects of fermentable high fiber diet supplementation on gut derived and conventional nitrogenous product in patients on maintenance hemodialysis: a randomized controlled trial – Hamid Tayebi Khosroshahi – Nutrition and Metabolism

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

The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda – Charissa C Naidoo – Lancet Respiratory medicine

Fecal Microbiota Transplantation: An Update on Clinical Practice – Kyeong Ok Kim – Clinical Endoscopy

Aryl hydrocarbon receptor and uremic toxins from gut microbiota in chronic kidney disease patients: Is there a relationship? – Jessyca Brito – Biochemistry

Animal experiments

Bacterial AB5 toxins inhibit the growth of gut bacteria by targeting ganglioside-like glycoconjugates – Robert T. Patry – Nature Communications

Simplified Intestinal Microbiota to Study Microbe-Diet-Host Interactions in a Mouse Model – Petia Kovatcheva-Datchary – Cell Reports

Pomegranate ellagitannin-gut microbial-derived metabolites, urolithins, inhibit neuroinflammation in vitro – Nicholas A. DaSilva – Nutritional Neuroscience

Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection – Eric M. Velazquez – Nature Microbiology

Plant, root, soil microbiome

Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly – Carolina Suarez – Scientific Reports

Untapped viral diversity in global soil metagenomes – Emily B. Graham – BioRxiv

Water microbiome and extremophiles

Fate of antibiotic resistance genes in two Arctic tundra wetlands impacted by municipal wastewater – Jennifer L. Hayward – Science of the Total Environment

Probiotics

Importance of probiotics in the prevention and treatment of colorectal cancer – Majid Eslami – Journal of Cellular Physiology

Non-microbiology picks

Artificial womb technology breaks its four minute mile – Science Daily

March 27, 2019

Happy Wednesday! Today’s digest includes spider endosymbionts, microbes shared between family members, and the effects of plastic on the microbiome of compost. Enjoy!

General microbiome

Transmission of human-associated microbiota along family and social networks – Brito – Nature Microbiology

Diversity-disease relationships and shared species analyses for human microbiome-associated diseases – Ma – ISME

Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity – Fodelianakis – Nature Communications

Preprint: Exploring the archaeome: detection of archaeal signatures in the human body – Pausan – bioRxiv

Human gut microbiome

Sucrose 6F-phosphate phosphorylase: a novel insight in the human gut microbiome – Tauzin – Microbial Genomics

Human skin microbiome

Preprint: Moving microbes: the dynamics of transient microbial residence on human skin – Vandegrift – bioRxiv

Animal experiments

Effects of phycocyanin in modulating the intestinal microbiota of mice – Xie – MicrobiologyOpen

Animal microbiome

Preprint: Endosymbiotic bacteria are prevalent and diverse in agricultural spiders – White – bioRxiv

Plant, root, and soil microbiome

Litter Quality Modulates Effects of Dissolved Nitrogen on Leaf Decomposition by Stream Microbial Communities – Jabiol – Microbial Ecology

Additions of sugar and nitrogenous fertiliser affect plant nitrogen status and soil microbial communities – Morrow – Applied Soil Ecology

Characterizing differences in microbial community composition and function between Fusarium wilt diseased and healthy soils under watermelon cultivation – Wang – Plant and Soil

Meta-analysis shows positive effects of plant diversity on microbial biomass and respiration – Chen – Nature Communications

Effects of transgenic glufosinate-tolerant rapeseed (Brassica napus L.) and the associated herbicide application on rhizospheric bacterial communities – Tang – Physiological and Molecular Plant Pathology

Structure and Diversity of Soil Bacterial Communities in Offshore Islands – Lin – Scientific Reports

The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China – Chen – Applied Microbiology and Biotechnology

Variation in rhizosphere priming and microbial growth and carbon use efficiency caused by wheat genotypes and temperatures – Yin – Soil Biology and Biochemistry

Using a soil bacterial species balance index to estimate potato crop productivity – Jeanne – PLoS One

Limited effect of planting transgenic rice on the soil microbiome studied by continuous 13CO2 labeling combined with high-throughput sequencing – Wang – Applied Microbiology and Biotechnology

Range-expansion effects on the belowground plant microbiome – Ramirez – Nature Ecology and Evolution

Water and extremophile microbiome

Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments – Marshall – ISME

Built environment

Exploring the long-term effect of plastic on compost microbiome – Esan – PLoS One

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced “iron mound” sediments – Leitholf – PLoS One

Probiotics/prebiotics

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling – Ansari – PLoS One

Review: Importance of probiotics in the prevention and treatment of colorectal cancer – Eslami – Journal of Cellular Physiology

Techniques

Robust sampling and preservation of DNA for microbial community profiling in field experiments – Groenenboom – BMC Research Notes

March 25, 2019

Good morning everyone! In today’s microbiome digest, we have multiple research and review articles about the role of microbiome in various diseases including neurodevelopmental, biliary Cholangitis, obesity-associated CRC, bariatric surgery, atopic dermatitis, schizophrenia, respiratory tract infection and autoimmunity, and an independent section on Fecal Microbiota Transplantation. Enjoy reading.

General microbiome

Talking about a microbiome revolution – John F. Cryn – Nature Microbiology

Review: Crosstalk between neutrophils and the microbiota – Dachuan Zhang – Blood

 Gut microbiome

Alteration of gut microbiota by a westernized lifestyle and its correlation with insulin resistance in non‐diabetic Japanese men – Mami Yamashita – Journal of Diabetes Investigation

Association of the Infant Gut Microbiome With Early Childhood Neurodevelopmental Outcomes – Joanne E. Sordillo – JAMA Netw Open

Comprehensive Analysis of Serum and Fecal Bile Acid Profiles and Interaction with Gut Microbiota in Primary Biliary Cholangitis – Weihua Chen – Clinical Reviews in Allergy & Immunology

Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC – K Leigh Greathouse – BMJ Open Gastroenterology

Gut microbiota specific signatures are related to the successful rate of bariatric surgery – Gutiérrez-Repiso C – American Journal of Transplantation Research

Differences in Systemic IgA Reactivity and Circulating Th Subsets in Healthy Volunteers With Specific Microbiota Enterotypes – Christina Grosserichter-Wagener – Frontiers in Immunology

Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture – Sofia Reddel – Scientific Reports

Prebiotic effect of predigested mango peel on gut microbiota assessed in a dynamic in vitromodel of the human colon (TIM-2) – Sonia G. Sáyago-Ayerdi – Food Research International

Review: The gut microbiota promotes the pathogenesis of schizophrenia via multiple pathways – Xiuxia Yuan – Biochemical and Biophysical Research Communications

Evidence for an association of gut microbial Clostridia with brain functional connectivity and gastrointestinal sensorimotor function in patients with irritable bowel syndrome, based on tripartite network analysis – Jennifer S. Labus – Microbiome

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome – Zhuye Jie – bioRxiv

Human respiratory microbiome

The microbiological characteristics of lower respiratory tract infection in patients with neuromuscular disorders: An investigation based on a multiplex polymerase chain reaction to detect viruses and a clone library analysis of the bacterial 16S rRNA gene sequence in sputum samples – Masato Ogawa – Journal of Microbiology, Immunology and Infection

Vaginal micorbiome

Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery – Michal A. Elovitz – Nature Communications

Animal microbiome / Animal experiments

Autoimmunity-Associated Gut Commensals Modulate Gut Permeability and Immunity in Humanized Mice – Baskar Balakrishnan – Military Medicine

Microbe and host interaction in gastrointestinal homeostasis – Rachael Horne – Psychopharmacology

Broiler gut microbiota and expressions of gut barrier genes affected by cereal type and phytogenic inclusion – VasileiosParaskeuas – Animal Nutrition

Manipulation of gut microbiota blunts the ventilatory response to hypercapnia in adult rats – Karen M. O’Connor – EbioMedicine

Beneficial Effects of Potentilla discolor Bunge Water Extract on Inflammatory Cytokines Release and Gut Microbiota in High-Fat Diet and Streptozotocin-Induced Type 2 Diabetic Mice – Lihua Han – Nutrients

Effects of gut-derived endotoxin on anxiety-like and repetitive behaviors in male and female mice – Christopher T. Fields – Biology of Sex Differences

Fecal Microbiota Transplantation

Recent Research on Fecal Microbiota Transplantation in Inflammatory Bowel Disease Patients – Monika Fischer – Gastroenterology and Hepatology

Assessing the viability of transplanted gut microbiota by sequential tagging with D-amino acid-based metabolic probes – Wei Wang – Nature Communications

Do we really understand how faecal microbiota transplantation works? Authors’ reply – Lito E. Papanicolas – EbioMeidicine

Water and extremophile microbiome

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing – You Che – Microbiome

Evolution of microbial community and drug resistance during enrichment of tetracycline-degrading bacteria – Qiang Wang – Ecotoxicology and Environmental Safety

Bioinformatics

A generic multivariate framework for the integration of microbiome longitudinal studies with other data types – Antoine Bodein – bioRxiv

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

 

March 20, 2019

Today’s digest features a longitudinal survey of maternal anti-viral antibodies in newborns that provides a blueprint for understanding infectious disease susceptibility, a detailed overview of antimicrobial resistance identification and characterization methods (from traditional antimicrobial susceptibility testing to recent deep-learning methods), and more. Happy reading!

Gut microbiome

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention – Jessica A Grembi – bioRxiv

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3 – Zheng Kuang – bioRxiv

*Neuronal programming by microbiota enables environmental regulation of intestinal motility – Yuuki Obata – bioRxiv

Probiotics

Growth Mode and Carbon Source Impact the Surfaceome Dynamics of Lactobacillus rhamnosus GG – Kirsi Savijoki – bioRxiv

Nasal microbiome

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

Vaginal microbiome

Mini review: Vaginal microbiota transplantation for the treatment of bacterial vaginosis: a conceptual analysis – Dongwen Ma – FEMS Microbiology Letters

Comparative study of vulva and abdominal skin microbiota of healthy females with high and average BMI – Rebecca Vongsa – BMC Microbiology

Plant/root/soil microbiome

Biosurfactant production by a rhizosphere bacteria Bacillus altitudinis MS16 and its promising emulsification and antifungal activity – Madhurankhi Goswami & Suresh Deka – Colloids and Surfaces B: Biointerfaces

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

Water microbiome

Ecological processes underpinning microbial community structure during exposure to subinhibitory level of triclosan – Seungdae Oh – Scientific Reports

Microbial Ecology of Snow Reveals Taxa-Specific Biogeographical Structure – Shawn P. Brown & Ari Jumpponen – Microbial Ecology

Phages and viruses

*The repertoire of maternal anti-viral antibodies in human newborns – Christian Pou – Nature Medicine

Methods

*Review: Sequencing-based methods and resources to study antimicrobial resistance – Manish Boolchandani – Nature Reviews Genetics