Category Archives: Human reproductive or urinary

May 30, 2019

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How the cheese rind microbiome diversity affects function, development of “metabolic overlap” as a metric to assess different microbial communities using genomic information, a variety of research articles, commentaries, press releases, and news stories covering the NIH Human Microbiome Project at the completion of its second phase.

General microbiome

Homepage for “Human Microbiome Project, part 2” special section in Nature including:

Human vaginal microbiome

The vaginal microbiome and preterm birth – Jennifer M Fettweis – Nature Medicine

Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy – Myrna G Serrano – Nature Medicine

Human gut microbiome

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases – Jason Lloyd-Price – Nature

Pre-print: Antioxidants maintain Butyrate production by Human Gut Clostridia in the presence of Oxygen – Matthieu Million – bioRxiv

A microbiota-generated bile salt induces biofilm formation in Clostridium difficile – Thomas Dubois – NPJ Biofilms and Microbiomes

Plant, root, and soil microbiome

Pre-print: Bacterial and fungal communities are differentially modified by melatonin in agricultural soils under abiotic stress – Andrew P Madigan – bioRxiv

Food microbiology

Pre-print: Strain-level diversity impacts cheese rind microbiome assembly and function – Brittany A Niccum – bioRxiv

Bioinformatics

Pre-print: Metabolic overlap in environmentally diverse microbial communities – Eric R Hester – bioRxiv

Microbes in the news

The Human Microbiome Project expands the toolbox for studying host and microbiome interactions – National Institutes of Health

A wave of NIH-backed microbiome research examines the gut’s link to diabetes, inflammatory bowel disease, and more – Kate Sheridan – STAT

Human Microbiome Project reveals how microbiome is disrupted during inflammatory bowel disease – Christopher Sweeney – Broad Institute

Scientists Find Bacteria Thriving In Earth Environment That’s Just Like Young Mars – Aristos Georgiou – Newsweek

May 29, 2019

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Changes to the pig gut microbiome based on age, gut bacteria community composition in aquatic invertebrates, fungal diversity on limestone cathedral walls, chalk-talk vs PowerPoint in large microbiology lectures.

Human oral microbiome

Applications of the oral microbiome in personalized dentistry – Georgios N Belibasakis – Archives of Oral Biology

Human vaginal microbiome

Detection of Methanobrevibacter smithii in vaginal samples collected from women diagnosed with bacterial vaginosis – Ghiles Grine – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Gut Microbial Dataset of a foraging tribe from rural West Bengal – insights into unadulterated and transitional microbial abundance – Sayak Ganguli – Data in Brief

Gut microbiome of pre-adolescent children of two ethnicities residing in three distant cities – Wei Wei Thwe Khine – Scientific Reports

The eradication of Helicobacter pylori restores rather than disturbs the gastrointestinal microbiota in asymptomatic young adults – Cong He – Helicobacter

Pre-print: Cytometric fingerprints of gut microbiota predict Crohn’s disease state – Peter Rubbens – bioRxiv

Animal experiments

Rapamycin modulates tissue aging and lifespan independently of the gut microbiota in Drosophila – Joseph M Schinaman – Scientific Reports

Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition – Shanlin Ke – BMC Veterinary Research

Pre-print: Effects of Five Products on Gut Microbiota and Short-Chain Fatty Acids of Obese Rats – Simin Tan – bioRxiv

Animal microbiome

Effect of different forage-to-concentrate ratios on ruminal bacterial structure and real-time methane production in sheep – Runhang Li – PLOS ONE

Pre-print: Microbiomes from feces vs. gut in aquatic vertebrates: distinct community compositions between substrates and preservation methods – Sten Anslan – bioRxiv

Plant, root, and soil microbiome

Glycoside Hydrolase Genes Are Required for Virulence of Agrobacterium tumefaciens on Bryophyllum daigremontiana and Tomato – Stephanie L Mathews – Applied and Environmental Microbiology

Effect of water-driven changes in rice rhizosphere on Cd lability in three soils with different pH – Jinjin Wang – Journal of Environmental Sciences

Impact of AMF Claroideoglomus etunicatum on the structure of fungal communities in the tomato rhizosphere – Agnieszka Jamiołkowska – Acta Mycologica

Effect of land use and carbonates on organic matter stabilization and microbial communities in Mediterranean soils – Mireia Martí-Roura – Geoderma

Pre-print: Close-Range Interactions Favor Growth in Random-Paired Extracted Soil Bacteria – Manupriyam Dubey – bioRxiv

Water and extremophile microbiome

New microbial lineages capable of carbon fixation and nutrient cycling in deep-sea sediments of the northern South China Sea – Jiao-Mei Huang – Applied and Environmental Microbiology

Pre-print: Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep – Guojie Cui – PeerJ

Taxonomic structure and potential nitrogen metabolism of microbial assemblage in a large hypereutrophic steppe lake – Xiaodong Qu – Environmental Science and Pollution Research

Built environment

Fungal diversity and distribution across distinct biodeterioration phenomena in limestone walls of the old cathedral of Coimbra, UNESCO World Heritage Site – João Trovão – International Biodeterioration & Biodegradation

Probiotics/prebiotics

Dietary probiotics have different effects on the composition of fecal microbiota in farmed raccoon dog (Nyctereutes procyonoides) and silver fox (Vulpes vulpes fulva) – Yongjia Peng – BMC Microbiology

Microbes in the news

Microbiome therapies could be the next frontier in medicine. But how exactly do you make them? – Kate Sheridan – STAT

Possible link between infant gut microbiome and development of allergies – Bob Yirka – Medical Xpress

Science, career, and publishing

Pre-print: Rock the Chalk: A five-year comparative analysis of a large microbiology lecture course reveals improved outcomes of chalk-talk compared to PowerPoint – Christopher M Waters – bioRxiv

May 22, 2019

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Today’s Digest is full of new perspectives on appropriate models and techniques, including the future of gnotobiotics and using unbiased metagenomics to find RNA viruses. There are also several plant, root, and soil papers, particularly examining the interplay between bacterial and fungal communities. Finally, enjoy a preprint about the cartography of antibiotic resistance genes in a hospital, a study examining the microbiota in larval mosquito vectors of malaria, and a paper about the microeukaryotes associated with coral reefs.

General Microbiome
Review: Antibiotics versus biofilm: an emerging battleground in microbial communities – Divakar Sharma – Antimicrobial Resistance & Infection Control

Review: Gnotobiotics: Past, present and future – Marijana Basic – Laboratory Animals

Review: The use of non-rodent model species in microbiota studies – Aaron C. Ericsson – Laboratory Animals

Pregnancy and Early Life
Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates – Esperanza Escribano – PLoS One

Human Vaginal Microbiome
Vaginal microbiota and mucosal pharmacokinetics of tenofovir in healthy women using tenofovir and tenofovir/levonorgestrel vaginal rings – Andrea Ries Thurman – PLoS One

Human Oral Microbiome
Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function – Claire Duvallet – PLoS One

Animal Microbiome
Color morphology of Diaphorina citri influences interactions with its bacterial endosymbionts and ‘Candidatus Liberibacter asiaticus’ – Saeed Hosseinzadeh – PLoS One

Conspecific coprophagy stimulates normal development in a germ-free model invertebrate – Benjamin C. Jahnes – PeerJ

Malaria vector species in Amazonian Peru co-occur in larval habitats but have distinct larval microbial communities – Catharine Prussing – PLoS Neglected Tropical Diseases

Animal Experiments
Gut and immune effects of bioactive milk factors in preterm pigs exposed to prenatal inflammation – Shuqiang Ren – American Journal of Physiology-Gastrointestinal and Liver Physiology

Effects of oregano essential oil on the ruminal pH and microbial population of sheep – Rui Zhou – PLoS One

Plant, Root, and Soil Microbiome
Characterizing the intra-vineyard variation of soil bacterial and fungal communities – Hebin Liang – Frontiers in Microbiology

The role of fungi in heterogeneous sediment microbial networks – Jenny Marie Booth – Scientific Reports

Altering N2O emissions by manipulating wheat root bacterial community – Alla Usyskin-Tonne – Scientific Reports

Sphingomonas sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis Thaliana Under Drought Stress – Yang Luo – Frontiers in Microbiology

Enrichment of soil rare bacteria in root by an invasive plant Ageratina adenophora – Lin Chen – Science of the Total Environment

Effect of rhizospheric and endophytic bacteria with multiple plant growth promoting traits on wheat growth – Somayeh Emami – Environmental Science and Pollution Research

Water and Extremophile Microbiome
A comparison of microeukaryote communities inhabiting sponges and seawater in a Taiwanese coral reef system – Daniel Francis Richard Cleary – Annals of Microbiology

An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa – K. Jordaan – PLoS One

Built Environment
Preprint: Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment – Kern Rei Chng – bioRxiv

Fungal community composition analysis of 24 different urban parks in Shanghai, China – Jing Zhang – Urban Ecosystems

Techniques
Expanding the RNA Virosphere by Unbiased Metagenomics – Yong-Zhen Zhang – Annual Review of Virology

Preprint: Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO – Alexander H. Wilcox – bioRxiv

Development of an autonomous biosampler to capture in situ aquatic microbiomes – Hugo Ribeiro – PLoS One

May 4, 2019

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Have a good weekend! Today, in this MB, we have interesting papers about different aspects of the microbiome. For example, we have a review overviewing the relationship between epigenetic changes, microbiome and metabolic diseases, as well as a paper focused in the use of a microbial metabolite in the prognosis of coronary issues. We have also the publication of an interesting study authored by the MB founder Elisabeth Bik.

There are also some papers about coral microbiome and an study about the homogenization of the microbiome between both US Air Force cadets and their built environment.

 

Human and General Microbiome

Review: Epigenetic Markers and Microbiota/Metabolite-Induced Epigenetic Modifications in the Pathogenesis of Obesity, Metabolic Syndrome, Type 2 Diabetes, and Non-alcoholic Fatty Liver Disease – Daniela Stols-Gonçalves – Current Diabetes Reports

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth Bik – PLoS ONE

Trimethyllysine, a trimethylamine N-oxide precursor, provides near- and long-term prognostic value in patients presenting with acute coronary syndromes – Xinmin S Li – European Heart Journal

Review: The interaction between Entamoeba histolytica and enterobacteria shed light on an ancient antibacterial response – Nancy Guillén – Cellular Microbiology

PCR Characterization of Microbiota on Contracted and Non-Contracted Breast Capsules – Yara Bachour – Aesthetic Plastic Surgery

Decreased Cephalosporin Susceptibility of Oropharyngeal Neisseria Species in Antibiotic-Using Men-who-have-sex-with-men of Hanoi, Vietnam– Huan V Dong – Clinical Infectious Diseases

Review: Smoking and periodontal microorganisms – Takashi Hanioka – Japanese Dental Science Review

The influence of the vaginal microbiota on preterm birth: A systematic review and recommendations for a minimum dataset for future research – Myrthe JCS. Peelen – Placenta

Gut Microbiome in Health and Disease: Emerging Diagnostic Opportunities – Aonghus Lavelle – Gastroenterology Clinics of North America

Laryngotracheal Microbiota in Adult Laryngotracheal Stenosis – Alexander T. Hillel – mSphere

Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes – Pedro Escudeiro –  mSphere

 

Beneficial Microbes

Review: Changing our microbiome: Probiotics in dermatology – Y. Yu – British Journal of Dermatology

Amelioration of obesity-related biomarkers by Lactobacillus sakei CJLS03 in a high-fat diet-induced obese murine model – Josep Ji – Scientific Reports

 

Animal Models / Animal Microbiome

Age-related analysis of the gut microbiome in a purebred dog colony – Keijiro Mizukami – FEMS Microbiology Letters

Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus) – Christina F. Butowski – PLoS ONE

Effects of diet on gut microbiota of soil collembolans – Qian Xiang – Science of The Total Environment

Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome – Rebecca L. Maher – Scientific Reports

Structure and stability of the coral microbiome in space and time – Courtney M. Dunphy – Scientific Reports

The effect of dissolved nickel and copper on the adult coral Acropora muricata and its microbiome – Francesca Gissi – Environmental Pollution

 

Food Microbiome

Microbiota and Chemical Compounds in Fermented Pinelliae Rhizoma (Banxiaqu) from Different Areas in the Sichuan Province, China – Bo Shu – Polish Journal of Microbiology

 

Built Environment

Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets –  Anukriti Sharma – Microbiome

 

Environmental Microbiome

The Influence of Temperature and Nitrogen Source on Cellulolytic Potential of Microbiota Isolated from Natural Environment –  Agnieszka Wita  – Polish Journal of Microbiology

 

Techniques

The potential of nanoflow liquid chromatography-nano electrospray ionisation-mass spectrometry for global profiling the faecal metabolome – Andrew J. Chetwynd – Journal of Chromatography A

May 3, 2019

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A concise Digest today featuring a novel approach to targeting antibiotic resistance, and some cool art by a Healthcare company to promote infectious disease awareness. Enjoy reading! (Apologies for the tight formatting, technological difficulty…)
General microbiology
Review: Fungal evolution: major ecological adaptations and evolutionary transitions – Miguel A. Naranjo-Ortiz and Toni Gabaldón – Biological Reviews
Antibiotic resistance
Pregnancy and early life
Household composition and the infant fecal microbiome: The INSPIRE study – Avery A. Lane et al. – American Journal of Physical Anthropology
Human skin microbiome
Human reproductive microbiome
Cancer microbiome
Review: Culture-independent studies on bacterial dysbiosis in oral and oropharyngeal squamous cell carcinoma: A systematic review – Divya Gopinatha & Rohit Kunnath Menonb et al. – Critical reviews Oncology Hematology
Animal experiments
Plant, root and soil microbiome
Microbes in the news
‘Microbiome’ May Be Key to Autism Symptoms – Serena Gordon – Health Day

 

May 2, 2019

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In today’s digest read about variations in milk and infant fecal microbiome (Ethiopia, Gambia, USA, Ghana, Kenya, Peru, Spain, and Sweden), the microbiome, metabolome, and lipidome of obese and non-obese horses (USA), and Bacteroides fragilis adaptive evolution (Western countries and China). Happy reading!

Pregnancy and birth

*What’s normal? Microbiomes in human milk and infant feces are related to each other but vary geographically: the INSPIRE study – Kimberly A. Lackey – Frontiers in Nutrition

Progesterone Increases Bifidobacterium Relative Abundance during Late Pregnancy – Meital Nuriel-Ohayon – Cell Reports

Gut microbiome

Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age – M Nazmul Huda – The Journal of nutrition

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age – Kent A. Willis – bioRxiv

*Adaptive Evolution within Gut Microbiomes of Healthy People – Shijie Zhao – Cell Host & Microbe

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders – George B. Saffouri – Nature Communications

Oral microbiome

Review: The Role of Exopolysaccharides in Oral Biofilms – C. Cugini – Journal of Dental Research

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes – Angela C. Poole – Cell Host & Microbe

Animal microbiome

*Comparison of the microbiome, metabolome, and lipidome of obese and non-obese horses – Michelle C. Coleman – PlosOne

Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning – Ubaldo De La Torre – PlosOne

Microbiome characterization of poultry products based on the poultry part and production label – Sang In Lee – FEMS Microbiology Letters

Metagenomic analysis of isolation methods of a targeted microbe, Campylobacter jejuni, from chicken feces with high microbial contamination – Junhyung Kim – Microbiome

Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health – H.Z.Sun – Journal of Dairy Science

Characterization of pig saliva as the major natural habitat of Streptococcus suis by analyzing oral, fecal, vaginal, and environmental microbiota – Kazunori Murase – PlosOne

Insight into the microbial world of Bemisia tabaci cryptic species complex and its relationships with its host – Hua-Ling Wang – Scientific Reports

Water and extremophile microbiome

The Plastisphere – Uncovering tightly attached plastic “specific” microorganisms – Inga Vanessa Kirstein – PlosOne

The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes – Han-Fei Tsao – Water Research

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities – Tim N.Enke – Current Biology

Impact of a river flood on marine water quality and planktonic microbial communities – Annamaria Zoppini – Estuarine, Coastal and Shelf Science

Microbial ecological processes in MBBR biofilms for biological phosphorus removal from wastewater – Knut Rudi – Water Science & Technology

Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany – Anita Perkins – bioRxiv

Plant/root/soil microbiome

The rice leaf microbiome has a conserved community structure controlled by complex host-microbe interactions – Veronica Roman-Reyna – bioRxiv

Spatial vs. temporal controls over soil fungal community similarity at continental and global scales – Colin Averil – The ISME Journal

Metabolomics Reveal that Engineered Nanomaterial Exposure in Soil Alters Both Soil Rhizosphere Metabolite Profiles and Maize Metabolic Pathways – Lijuan Zhao – Environmental Science: Nano

High-throughput sequencing reveals the diversity and community structure of rhizosphere fungi of Ferula Sinkiangensis at different soil depths – Tao Zhang – Scientific Reports

Microplastics can change soil properties and affect plant performance – Anderson Abel de Souza Machado – Environmental Science and Technology

April 28, 2019

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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

April 13, 2019

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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

8 April, 2019

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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.

April 6, 2019

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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