April 15, 2019

Today’s Monday morning digest covers reviews on different aspects of human microbiome, interesting articles about effects of early life treatments in rodents and news updates on market prediction of microbiome sequencing and therapeutics.

General microbiome

Current understanding of the human microbiome – Jack A Gilbert – Nature Communications

The Importance of the Microbiome in Bariatric Surgery: a Systematic Review – Josianne C. H. B. M. Luijten – Obesity surgery

A potential role for the gut microbiome in substance use disorders – Katherine R. Meckel – Psychopharmacology

The power of small changes: Comprehensive analyses of microbial dysbiosis in breast cancer – Sheetal Parida -Biochimica et Biophysica Acta

The lung microbiome and transplantation –  Alicia B. Mitchell – Current Opinion in Organ Transplantation

Human gut microbiome

Encrustations on ureteral stents from patients without urinary tract infection reveal distinct urotypes and a low bacterial load – Matthias T. Buhmann – Microbiome

Overuse of anti‐anaerobic drug is associated with poor post‐chemotherapy prognosis of patients with hepatocellular carcinoma – Noriho Lida – International Journal of Cancer

Antibiotic-induced shifts in fecal microbiota density and composition during hematopoietic stem cell transplantation – Sejal Morjaria – BioRxiv

Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit – AJH Cremers – BioRxiv

Animal experiments

Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior – Iva Lukić – Translational Psychiatry

Early life stress induces type 2 diabetes-like features in ageing mice – Hanna Ilchmann-Diounou – Brain, Behavior and Immunity

Early-life vancomycin treatment promotes airway inflammation and impairs microbiome homeostasis – Xin Yang – Aging

Early-life stress, microbiota, and brain development: probiotics reverse the effects of maternal separation on neural circuits underpinning fear expression and extinction in infant rats – Caitlin S.M. Cowan – Developmental Cognitive Neuroscience

Commensal Escherichia coli aggravates acute necrotizing pancreatitis through targeting intestinal epithelial cells – Junyuan Zheng – Applied and Environmental Microbiology

Host-Microbiome Synergistic Control on Sphingolipid Metabolism by Mechanotransduction in Model Arthritis – Xiaoyuan Zhou – Biomolecules

Plant, root, soil microbiome

Bacterial community diversity associated with the severity of bacterial wilt disease in tomato fields in south-east China – Xuefang Zheng – Canadian Journal of Microbiology

Bacterial disease induced changes in fungal communities of olive tree twigs depend on host genotype – Teresa Gomes – Scientific Reports

Co‐inoculation of Bacillus spp. and Pseudomonas putida at different development stages acts as a biostimulant to promote growth, yield and nutrient uptake of tomato – Yanhui He – Journal of Applied Microbiology

Water microbiome and extremophiles

Extant microbial communities in the partially desiccated Rincon de Parangueo maar crater lake in Mexico – Janet Sánchez-Sánchez – Fems Microbiology Ecology

Novosphingobium meiothermophilum sp. nov., isolated from a hot spring – Wen-Dong Xian – International Journal of Systematic and Evolutionary Microbiology

Built Environment

Impacts of Indoor Surface Finishes on Bacterial Viability – Jinglin Hu – Indoor air

Probiotics

Probiotics: If It Does Not Help It Does Not Do Any Harm. Really? – Aaron Lerner – Microorganisms

Effects of Lactobacillus plantarum PS128 on Children with Autism Spectrum Disorder in Taiwan: A Randomized, Double-Blind, Placebo-Controlled Trial – Yen-Wenn Liu – Nutrients

Microbes in the news

Global Human Microbiome Therapeutics Market Outlook 2019-2024: ENTEROME Bioscience, Rebiotix, Seres Therapeutics – NewsPrimo

Caesarean babies slower to acquire ‘good’ gut bacteria: study – PanArmenian Net

Mode of delivery has substantial impact on infants’ health – Business Standard

Newborn’s ‘Microbiome’ Could Give Clues to Weight Later – Doctors Lounge

Microbiome Sequencing Services Market is expected to grow at a CAGR of 18% during the forecast period of (2018 – 2023) – Redfield Report

Human Microbiome Market boosting the growth Worldwide – Business Herald

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April 13, 2019

In today’s digest read about diverse population of bacteria and fungi on the International Space Station, how antidepressants affect gut microbiota, and check out a new framework for comparing and assessing taxonomic profilers (OPAL). Happy weekend!

Vaginal microbiome

Defining characteristics of genital health in South African adolescent girls and young women at high risk for HIV infection – Smritee Dabee – PlosOne

Detection of ureaplasmas and bacterial vaginosis associated bacteria and their association with non-gonococcal urethritis in men – Maria Frølund – PlosOne

Group B streptococcal screening, intrapartum antibiotic prophylaxis, and neonatal early-onset infection rates in an Australian local health district: 2006-2016 – Kathryn Braye – PlosOne

Gut microbiome

Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota – Dae-Wook Kang – Scientific Reports

The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations – Adrian Tett – bioRxiv

Fecal short-chain fatty acids are not predictive of colonic tumor status and cannot be predicted based on bacterial community structure – Marc A. Sze – bioRxiv

Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang – bioRxiv

Animal microbiome

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms – Philipp Rausch – bioRxiv

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 – Maria B. Grieco – Current Microbiolgy

The sponge microbiome within the greater coral reef microbial metacommunity – Daniel F. R. Cleary – Nature Communications

Insights into the intestinal microbiota of several aquatic organisms and association with the surrounding environment – Fulin Sun – Aquaculture

Animal experiments

*Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior – Iva Lukić – Translational Psychiatry

Chronic paradoxical sleep deprivation-induced depression­like behavior, energy metabolism and microbial changes in rats – Weini Ma – Life Sciences

Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota – Giulia Alessandri – Scientific Reports

Probiotics

Fasting breath H2 and gut microbiota metabolic potential are associated with the response to a fermented milk product in irritable bowel syndrome – Boris Le Nevé – PlosOne

Lactobacillus fermentum and Lactobacillus plantarum increased gut microbiota diversity and functionality, and mitigated Enterobacteriaceae, in a mouse model – C. Linninge – Beneficial Microbes

Complex responses to inflammatory oxidants by the probiotic bacterium Lactobacillus reuteri – Poulami Basu Thaku – bioRxiv

Plant/root/soil microbiome

Urban traffic changes the biodiversity, abundance, and activity of phyllospheric nitrogen-fixing bacteria – Yang Li – Environmental Science and Pollution Research

Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean – Shaohua Shi – Archives of Microbiology

Copper and zinc in rhizospheric soil of wild plants growing in long-term acid vineyard soils – C.Campillo-Cora – Science of The Total Environment

Review: Soil microbiome: a key player for conservation of soil health under changing climate – Anamika Dubey – Biodiversity and Conservation

Rhizosphere microbiota compositional changes reflect potato blackleg disease – Lutian Mao – Applied Soil Ecology

Pseudomonas urumqiensis sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia – Yuanyuan Zou – International Journal of Systematic and Evolutionary Microbiology

Insights gained from metagenomic shotgun sequencing of apple fruit epiphytic microbiota – Dario Angeli – Postharvest Biology and Technology

Extremophile microbiome

*Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces – Aleksandra Checinska Sielaff – Microbiome

Techniques

Review: Untargeted LC/MS-based metabolic phenotyping (metabonomics/metabolomics): The state of the art – Helen Gika – Journal of Chromatography B

Bioinformatics

*Assessing taxonomic metagenome profilers with OPAL – Fernando Meyer – Genome Biology

Analysis of error profiles in deep next-generation sequencing data – Xiaotu Ma – Genome Biology

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers – Kieran R. Campbell – Genome Biology

RnBeads 2.0: comprehensive analysis of DNA methylation data – Fabian Müller – Genome Biology

Review: Big data analytics for personalized medicine – Davide Cirillo and Alfonso Valencia – Current Opinion in Biotechnology

Meta-network: optimized species-species network analysis for microbial communities – Pengshuo Yang – BMC Genomics

April 6, 2019

Highlights: Inferring absolute species concentration in vaginal microbiome, transcriptomics of Arctic Tundra soils, successional traits of prokaryotic communities in Tundra soil, Modulation of plant microbial community by fungal endophyte Epichloë and many more.

General microbiome

Microbial community design: methods, applications, and opportunities –  A Eng – Current Opinion in Biotechnology

Human vaginal microbiome

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota – Charlotte van der Veer – Microbiome

Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome – Florencia Tettamanti Boshier – bioRxiv

Human gut microbiome

Perturbation of the human gut microbiome by a non-antibiotic drug contributes to the resolution of autoimmune disease – Renuka R Nayak – bioRxiv

Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection – SX Li – PLoS Pathogens

Distinct gut microbiota profile in antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers – L Sessa – AIDS

The relationship between gastric microbiota and gastric disease – S Zhang – Scandinavian Journal of Gastroenterology

The Gut Microbiome Says NO to microRNA-Mediated Gene Silencing – Z Wei – Biochemistry

Functional diversity and metabolic profile of microbial community of mine soils with different levels of chromium contamination – SK Pradhan – International Journal of Environmental Health Research

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil – AW Bowsher – mSystems

Spatial segregation of the biological soil crust microbiome around its foundational cyanobacterium, Microcoleus vaginatus, and the formation of a nitrogen-fixing cyanosphere – E Couradeau – Microbiome

 

Plant, root, and soil microbiome

A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides – Barbara Cania – Environmental Microbiome

Heritable Epichloë symbiosis shapes fungal but not bacterial communities of plant leaves – Riitta Nissinen – Scientific Reports

Prokaryotic community shifts during soil formation on sands in the tundra zone – Alena Zhelezova – PLoS ONE

The epiphytic microbiota of sour rot-affected grapes differs minimally from that of healthy grapes, indicating causal organisms are already present on healthy berries – Megan E Hall – PLoS ONE

Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome – Morten Dencker Schostag – bioRxiv

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil – Evan P. Starr – bioRxiv

Comparison of prokaryotic communities between the fields showing different disinfestation effects by anaerobic soil disinfestation – Chol Gyu Lee – bioRxiv

Long-term urea fertilization alters the composition and increases the abundance of soil ureolytic bacterial communities in an upland soil – R Sun – FEMS Microbial Ecology

Water and extremophile microbiome 

Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities – Sergei Belikov – PLoS ONE

Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria – B Paix – Environmental Microbiology

Monitoring Microbial Communities in the Marine Environment – Ger van den Engh – Cytometry Part A

Microbes in the news

Evidence for link between ‘leaky gut’ and autoantibody production in HIV-positive patients – Science Daily

Eden Project hosts bacteria filled art exhibition – The Packet

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 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 7, 2019

Happy Thursday! Today’s digest includes the tree shrew gut virome, microbial communities in hummingbird feeders, and the relationship between oral microbes and taste. Enjoy!

Human gut microbiome

Human Gut Microbiome Response Induced by Fermented Dairy Product Intake in Healthy Volunteers – Volokh – Nutrients

Human oral microbiome

New insights into the relationship between taste perception and oral microbiota composition – Cattaneo – Scientific Reports

Animal experiments

Linseed oil and heated linseed grain supplements have different effects on rumen bacterial community structures and fatty acid profiles in cashmere kids – Wang – Journal of Animal Science

Microbiota Depletion Impairs Thermogenesis of Brown Adipose Tissue and Browning of White Adipose Tissue – Li – Cell Reports

Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology – Rangan – Cell Reports

The gut microbiota composition affects dietary polyphenols-mediated cognitive resilience in mice by modulating the bioavailability of phenolic acids – Frolinger – Scientific Reports

Animal microbiome

Characteristics of the tree shrew gut virome – Chen – PLoS One

Contact with adult hen affects development of caecal microbiota in newly hatched chicks – Kubasova – PLoS One

The Bos taurus maternal microbiome: Role in determining the progeny early-life upper respiratory tract microbiome and health – Ferreira Lima – PLoS One

Microbial diversity in the tick Argas japonicus (Acari: Argasidae) with a focus on Rickettsia pathogens – Yan – medical and Veterinary Entomology

Microbial communities in hummingbird feeders are distinct from floral nectar and influenced by bird visitation – Lee – Proceedings of the Royal Society B: Biological Sciences

Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments – Liu – Scientific Reports

Plant, root, and soil microbiome

Potential role of weather, soil and plant microbial communities in rapid decline of apple trees – Singh – PLoS One

Plant Materials are Sustainable Substrates Supporting New Technologies of Plant-Only-Based Culture Media for in vitro Culturing of the Plant Microbiota – Mourad – Microbes and Environments

Variation in soil fungal community structure during successive rotations of Casuarina equisetifolia plantations as determined by high-throughput sequencing analysis – Liuting – Plant Growth Regulation

Exploring the links between bacterial communities and magnetic susceptibility in bulk soil and rhizosphere of beech (Fagus sylvatica L.) – Chiellini – Applied Soil Ecology

The structure of denitrifying microbial communities in constructed mangrove wetlands in response to fluctuating salinities – Fu – Journal of Environmental Management

Water and extremophile microbiome

A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars – Cockell – Astrobiology

Microbial responses to anthropogenic dissolved organic carbon in Arctic and Antarctic coastal seawaters – Cerro‐Gálvez – Environmental Microbiology

Techniques

Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior – Lozano – MBio

A theoretical framework for controlling complex microbial communities – Tulio Angulo – Nature Communications

March 6, 2019

In today’s digest read how DNA polymerase and number of rounds of amplification in PCR affect 16S rRNA gene sequence data, how urinary microbiota changes after Cesarean delivery, how diverse is microbial community of thermal pools in Kamchatka (Russia), and more. Enjoy!

General microbiome

Toward multiomics-based next-generation diagnostics for precision medicine – Qi Wang – Personalized Medicine

Pregnancy and early life

*Alterations in the Urinary Microbiota Are Associated With Cesarean Delivery
Fengping Liu – Frontiers in Microbiology

Antimicrobial susceptibility and serotype distribution of Streptococcus agalactiae recto-vaginal colonizing isolates from pregnant women at a tertiary hospital in Pretoria, South Africa: an observational descriptive study letter – Mohamed Said – bioRxiv

Gut microbiome

Interplay between the human gut microbiome and host metabolism – Alessia Visconti – bioRxiv

A decrease in iron availability to human gut microbiome reduces the growth of potentially pathogenic gut bacteria; an in vitro colonic fermentation study – Bhavika A Parmanand – The Journal of Nutritional Biochemistry

Volatile organic compounds emitted from faeces as a biomarker for colorectal cancer – Ashley Bond – Alimentary Pharmacology and Therapeutics

Animal experiments

Loading ceftriaxone, vancomycin, and Bifidobacteria bifidum TMC3115 to neonatal mice could differently and consequently affect intestinal microbiota and immunity in adulthood – RuYue Cheng – Scientific Reports

Probiotics/Prebiotics

Prebiotics from acorn and sago prevent high-fat-diet-induced insulin resistance via microbiome–gut–brain axis modulation – Shokouh Ahmadi – The Journal of Nutritional Biochemistry

Viruses

A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data – Umberto Rosani – Viruses

Untargeted metabolomics analysis of the upper respiratory tract of ferrets following influenza A virus infection and oseltamivir treatment – David J. Beale – Metabolomics

Techniques

*The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data – Marc A Sze & Patrick D Schloss – bioRxiv

Utilisation of Ambient Laser Desorption Ionisation Mass Spectrometry (ALDI-MS) Improves Lipid-Based Microbial Species Level Identification – Simon J. S. Cameron – Scientific Reports

Animal microbiome

Characterization of the otic bacterial microbiota in dogs with otitis externa compared to healthy individuals – Juraj Korbelik – Veterinary Dermatology

Water and extremophile microbiome

*Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia – Laetitia G. E. Wilkins – Scientific Reports