September 30, 2019

Monday morning digest covers exciting updates in microbiome with – meta analysis on role of probiotics in human depression , stool banking guidelines for fecal microbiota transplant, expert view on translation of gut microbiome to clinics and a historical peek into use of ceramic baby milk bottles in prehistoric times. Enjoy reading!

General microbiome

Translating the gut microbiome: ready for the clinic? – Susan V. Lynch – Nature Reviews Gatroenterology and Hepatology

Uterine immunity and microbiota: A shifting paradigm – Chiara Agostinis – Frontiers in Immunology

Human microbiome

Cigarette smoking and oral microbiota in low-income and African-American populations – Yaohua Yang – Journal of Epidemiology and Community Health

International consensus conference on stool banking for faecal microbiota transplantation in clinical practice – Giovanni Cammarota – Gut

Animal experiments

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

Transfusional iron overload and intravenous iron infusions modify the mouse gut microbiota similarly to dietary iron – Francesca La Carpia – Biofilms and Microbiomes

Proteome modifications of gut microbiota in mice with activity-based anorexia and starvation: Role in ATP production – Jonathan Breton – Nutrition

Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut – Ulla Hynönen – Anaerobe

Intestinal inflammation increases convulsant activity and reduces antiepileptic drug efficacy in a mouse model of epilepsy – Carmen De Caro – Scientific Reports

The fecal resistome of dairy cattle is associated with diet during nursing – Jinxin Liu – Nature Communications

Neohesperidin Prevents Colorectal Tumorigenesis by Altering the Gut Microbiota – Yanling Gong – Pharmacological Research

Changes of serum lipopolysaccharide, inflammatory factors, and cecal microbiota in obese rats with type 2 diabetes induced by Roux-en-Y gastric bypass – Jiao Wu – Nutrition

Plant, root, soil microbiome

A bioinformatics guide to plant microbiome analysis – Rares Lucaciu – Frontiers in Plant Science

Beyond pathogens: microbiota interactions with the plant immune system – Paulo José PL Teixeira – Current Opinion in Microbiology

Water microbiome

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea‐land transition – Esther Molina-Menor – Microbial Biotechnology

Probiotics

Bacillus coagulans R11 maintained intestinal villus health and decreased intestinal injury in lead-exposed mice by regulating the intestinal microbiota and influenced the function of faecal microRNAs – Si-Cheng Xing – Environmental Pollution

Effect of probiotics on depressive symptoms: A meta-analysis of human studies – Kah Kheng Goh – Psychiatry Research

Non Microbiology Picks

Milk of ruminants in ceramic baby bottles from prehistoric child graves – J. Dunne – Nature

 

September 28, 2019

Dear microbiome digest readers, on this weekend we have covered interesting review articles focusing on factors that influence the temporal development of the infant microbiome, and  the role of gut microbiota in colorectal cancer, and research articles shows the role of microbiome in managing constipation, in Atopic Dermatitis, microbiome-host interaction in Respiratory Syncytial Virus Infection, Successful fecal microbiota transplantation for the treatment of recurrent Clostridium difficile infection, sputum microbiome in asthma and COPD and various research articles from Animal microbiome/Animal experiments section including fine-scale spatial structuring of the microbial composition and diversity along the length of murine colon. Enjoy reading.

General microbiome

Impact of a Plant Sterol- and Galactooligosaccharide-Enriched Beverage on Colonic Metabolism and Gut Microbiota Composition Using an In Vitro Dynamic Model – Virginia Blanco-Morales – Journal of Agricultural and Food Chemistry

Review: Temporal development of the infant gut microbiome – Rebecca E. Moore – Open Biology

Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform – Petra Videnska – Scientific Reports

The Honeybee Gut Microbiota Is Altered after Chronic Exposure to Different Families of Insecticides and Infection by Nosema ceranaeRégis Rouzé – Microbes and Environments

Human gut microbiome

Abundance of Probiotics and Butyrate‐Production Microbiome Manages Constipation Via Short‐Chain Fatty Acids Production and Hormones Secretion – Min Zhuang – Molecular Nutrition & Food Research

Review: Gut microbiota in colorectal cancer: mechanisms of action and clinical applications – Sunny H. Wong – Nature Reviews Gastroenterology & Hepatology

Changes in the gut microbiota during and after commercial helium-oxygen saturation diving in China – Yuan Y – Occupational and Environmental Medicine

Ninety-eight years old female successfully successfully treated with fecal microbiota transplantation after recurrent Clostridium difficile infection – Bermejo Boixareu C – Medicina Clínica

Human respiratory microbiome

Sputum microbiomic clustering in asthma and COPD reveals a Haemophilus‐predominant subgroup – Sarah Diver – Allergy

Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection – Abhijeet R. Sonawane – Scientific Reports

Human skin microbiome

Cheek Microbial Communities Vary in Young Children with Atopic Dermatitis in China – Song L. – Dermatology

Animal microbiome / Animal experiments

Dietary supplementation with the extract from Eucommia ulmoides leaves changed epithelial restitution and gut microbial community and composition of weanling piglets – Peng M – PLoS One

Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale – Sarah Goertz – PLoS One

Protective activities of polysaccharides from Cipangopaludina chinensis against high-fat-diet-induced atherosclerosis via regulating gut microbiota in ApoE-deficient mice – Qingping Xiong – Food & Function

2-O-beta-D-Glucopyranosyl-L-ascorbic acid, an Ascorbic Acid Derivative Isolated from the Fruits of Lycium Barbarum L., Modulates Gut Microbiota and Palliates Colitis in Dextran Sodium Sulfate-induced Colitis in Mice – Kaiyin Huang – Journal of Agricultural and Food Chemistry

Anti‐TNF‐α therapy alters the gut microbiota in proteoglycan‐induced ankylosing spondylitis in mice – Bin Liu – MicrobiologyOpen

A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome – Alessandra Riva – Nature Communication

Antibiotic exposure disturbs the gut microbiota and its metabolic phenotype differently in rats with advanced-stage type 1 diabetes and age-matched controls – Hong Zheng – Journal of Proteome Research

Gut Microbiota and Metabolome Response of Decaisnea insignis Seed Oil on Metabolism Disorder Induced by Excess Alcohol Consumption – Xiaoxia LiuJournal of Agricultural and Food Chemistry

Microbiome news

Vaginal Microbiome and Women’s Health: More Research Needed

NAU researchers aim to find microbial link between two common respiratory diseases

September 26, 2019

Have a nice day! Today, in this digest we have a good number of papers, including those associated with beneficial microbes, compounds, and interventions. Some highlights: host-microbiome evolution, microbiome and urinary tract infections, the first reported bloodstream infection caused by gut-habiting Prevotella species, microbiome activity in halitosis, and more! Enjoy.   

 

General or Human Microbiome

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

Review: Diagnosis of Urinary Tract Infection in the Neuropathic Bladder: Changing the Paradigm to Include the Microbiome – Catherine S. Forster – Topics in Spinal Cord Injury Rehabilitation 

Review: A critical review on diet-induced microbiota changes and cardiovascular diseases – Muthukumaran Jayachandran – Critical Reviews in Food Science and Nutrition 

Review: Microbiota: a novel regulator of pain – Manon Defaye – Journal of Neural Transmission

Relationship of tongue coating microbiome on volatile sulfur compounds in healthy and halitosis adults – Wei Ye – Journal of Breath Research

An Infectious Diseases Perspective on Fecal Microbiota Transplantation for Clostridioides difficile Infection in Children – Jillian M Cotter – Journal of the Pediatric Infectious Diseases Society

First bloodstream infection caused by Prevotella copri in a heart failure elderly patient with Prevotella-dominated gut microbiota: a case report – Patrizia Posteraro – Gut Pathogens

Pain regulation by gut microbiota: molecular mechanisms and therapeutic potential – Ran Guo – British Journal of Anaesthesia

The Dysbiosis and Inter-Kingdom Synergy Model in Oropharyngeal Candidiasis, a New Perspective in Pathogenesis – Martinna Bertolini – Journal of Fungi

Microbiome Influence in the Pathogenesis of Prion and Alzheimer’s Diseases – Valeria D’Argenio – International Journal of Molecular Sciences

Protein Intake at Twice the RDA in Older Men Increases Circulatory Concentrations of the Microbiome Metabolite Trimethylamine-N-Oxide (TMAO) – Sarah M. Mitchell – Nutrients

Potential Strategies in the Prevention of Nonsteroidal Anti-inflammatory Drugs-Associated Adverse Effects in the Lower Gastrointestinal Tract – Chuan-Guo Guo – Gut and Liver

 

Composition of gut microbiota of children and adolescents with perinatal HIV infection taking antiretroviral therapy in Zimbabwe – Trym T Flygel – The Journal of Infectious Diseases

Gut Microbiome in Psoriasis is Perturbed Differently During Secukinumab and Ustekinumab Therapy and Associated with Response to Treatment – Nai-Lun Yeh – Clinical Drug Investigation

The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants – Masaru Tanaka – Gut Microbes

 

Animal Microbiome

Food Preservatives Induce Proteobacteria Dysbiosis in Human-Microbiota Associated Nod2-Deficient Mice – Lucia Hrncirova – Microorganisms

Maternal Dietary Protein Intake Influences Milk and Offspring Gut Microbial Diversity in a Rat (Rattus norvegicus) Model –  Matthew F. Warren – Nutrients

Microbiota, Gut Health and Chicken Productivity: What Is the Connection? – Juan M. Diaz Carrasco – Microorganisms

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets – Raphaële Gresse – Microorganisms 

Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring – Pedro Soares-Castro – Scientific Reports

Core gut microbial communities are maintained by beneficial interactions and strain variability in fish – Fotini Kokou – Nature Microbiology

Beneficial Microbes and Compounds

Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly – Kerry L. Ivey – mBio

Oral Administration of β-Glucan and Lactobacillus plantarum Alleviates Atopic Dermatitis-like Symptoms – In Sung Kim – Journal of Microbiology and Biotechnology

Protective Effect of Probiotic Bacteria and Estrogen in Preventing HIV-1-Mediated Impairment of Epithelial Barrier Integrity in Female Genital Tract – Sara Dizzell – Cells (MPDI)

Fish Oil, but Not Olive Oil, Ameliorates Depressive-Like Behavior and Gut Microbiota Dysbiosis in Rats under Chronic Mild Stress – Te-Hsuan Tung – Biomolecules

The Potential Impact of Probiotics on the Gut Microbiome of Athletes – Laura Wosinska – Nutrients

Royal Jelly and Its Components Promote Healthy Aging and Longevity: From Animal Models to Humans – Hiroshi Kunugi – International Journal of Molecular Sciences

Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond – Carrie A. M. Wegh – International Journal of Molecular Sciences

Antifungal and Antivirulence Activity of Vaginal Lactobacillus Spp. Products against Candida Vaginal Isolates – Camilla Itapary dos Santos – Pathogens

Metabolic and Vascular Effect of the Mediterranean Diet – Antonino Tuttolomondo – International Journal of Molecular Sciences

 

Environmental Microbiome

Unveiling resistome profiles in the sediments of an Antarctic volcanic island – V.B. Centurion – Environmental Pollution

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea – Nojood A. Aalismail – Scientific Reports

 

Bioinformatics

The EFI Web Resource for Genomic Enzymology Web Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways – Rémi Zallot – Biochemistry

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification – Florian P Breitwieser – Biochemistry

 

Methods

Review: Common principles and best practices for engineering microbiomes – Christopher E. Lawson – Nature Reviews Microbiology

Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome – Oskar Hickl – Microorganisms

Optimizing bacterial DNA extraction in urine – Matthew M. Munch – PLoS One

 

September 24, 2019

Today’s digest is about diet-microbiota interactions in personalized  nutrition, interesting story on single bacterium association with fatty liver disease and how the gut microbiota adapt to red meat consumption.

General microbiome

Diet–microbiota interactions and personalized nutrition – Aleksandra A. Kolodziejczyk – Nature Reviews Microbiology

Citrobacter rodentium–host–microbiota interactions: immunity, bioenergetics and metabolism – Caroline Mullineaux-Sanders – Nature Reviews Microbiology

The interaction between the gut Microbiota and herbal medicines – Xuedong An – Biomedicine & Pharmacotherapy

Gut microbiota: what is its place in pharmacology? – Aleksandra Tarasiuk – Expert Review of Clinical Pharmacology

Human microbiome

Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae – Jing Yuan – Cell Metabolism

Association of Alterations in Intestinal Microbiota With Impaired Psychological Function in Patients With Inflammatory Bowel Diseases in Remission – Fabienne Humbel – Clinical Gastroenterology and Hepatology

Butyrate‐Producing Gut Bacteria and Viral Infections in Kidney Transplant Recipients: A Pilot Study – John R. Lee – Transplant Infectious Disease

Metabolomics and Microbial Composition Increase Insight into the Impact of Dietary Differences in Cirrhosis – I. Jane Cox – Liver International

Animal experiments

Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates – Livia S. Zaramela – Nature Microbiology

A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota – Weijun Wang – Scientific Reports

Comparative analysis of the fecal microbiota from different species of domesticated and wild suids – Florencia Correa-Fiz – Scientific Reports

Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing – Sofiya G. Shevchenko- Applied and Environmental Microbiology

Saponins from Clematis mandshurica Rupr. regulates gut microbiota and its metabolites during alleviation of collagen-induced arthritis in rats – Lin-Xiu Guo – Pharamacological Research

MHC Class II Antigen Presentation by the Intestinal Epithelium Initiates Graft-versus-Host Disease and Is Influenced by the Microbiota – Motoko Koyama – Immunity

Metformin Alters the Duodenal Microbiome and Decreases the Incidence of Pancreatic Ductal Adenocarcinoma Promoted by Diet-induced Obesity – Tien S Dong – American Journal of Physiology

Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach – Maria Guirro – PlosOne

Short-chain fatty acids and microbiota metabolites attenuate ghrelin receptor signaling – Cristina Torres-Fuentes – Faseb Journal

Effects of berberine and metformin on intestinal inflammation and gut microbiome composition in db/db mice – Wang Zhang – Biomedicine & Pharmacotherapy

Plant, root, soil microbiome

Water-soluble mercury induced by organic amendments affected microbial community assemblage in mercury-polluted paddy soil – Hualing Hu – Chemosphere

Phyllosphere colonisation by a soil Streptomyces sp. promotes plant defense responses against fungal infection – Sophie Vergnes – Molecular Plant-Microbe Interactions

Water microbiome 

Heat‐induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea – Wirulda Pootakham – Microbiology Open

Probiotics
Metabolomic profiling of oxalate-degrading probiotic Lactobacillus acidophilus and Lactobacillus gasseri – Casey A. Chamberlain – PlosOne

Probiotic Bifidobacterium bifidum G9‐1 ameliorates phytohemagglutinin‐induced diarrhea caused by intestinal dysbiosis -Yutaka Makizaki – Microbiology and Immunology

September 23, 2019

This Monday, check out the largest ever study of neonatal microbiomes, the study where researchers alter mouse gut microbiomes by feeding good bacteria their preferred fibers, and the study about the significant effect of antibiotics, antivirals and cofactors on the gut microbiome. Happy reading!

Pregnancy and early life

*Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth – Yan Shao – Nature

Gut microbiome

*Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans – Michael Patnode – Cell

*Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study – Matthias Willmann – BMC Biology

Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus – Feng Zhu – bioRxiv

Fecal Microbiotas of Indonesian and New Zealand Children Differ in Complexity and Bifidobacterial Taxa during the First Year of Life – Blair Lawley – Applied and Environmental Microbiology

Light-entrained and brain-tuned circadian circuits regulate ILC3s and gut homeostasis – Cristina Godinho-Silva – Nature

Baseline human gut microbiota profile in healthy people and standard reporting template – Charles H. King – PlosOne

Oral microbiome

Taste perception and oral microbiota are associated with obesity in children and adolescents – Chiara Mameli – PlosOne

Urinary microbiome

The urobiome of continent adult women: a cross-sectional study – Travis Price – Obstetrics & Gynaecology

The Urinary Microbiota in Relation to the Reproductive Tract Microbiota – Fei Li – bioRxiv

Respiratory microbiome

The effects of e-cigarette vapor exposure on the transcriptome and virulence of Streptococcus pneumoniae – Kamal Bagale – bioRxiv

Water microbiome

Diversity patterns of marine heterotrophic culturable bacteria along vertical and latitudinal gradients – Isabel Sanz-Sáez – bioRxiv

Laundry wastewater and domestic sewage pilot-scale anaerobic treatment: Microbial community resilience regarding sulfide production – A.G.L. Moura – Journal of Environmental Management

Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances – G. Gionchetta – Scientific reports

Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes – Parul Mittal – Environmental Microbiome

Plant/root/soil microbiome

Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome – Xiaoxuan Guo – Plant Communications

Metatranscriptomics reveals climate change effects on the rhizosphere microbiomes in European grassland – Qicheng Bei – Soil Biology and Biochemistry

Phages and viruses

Beyond cells – The virome in the human holobiont – Rodrigo García-López – Microbial cells

ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples – Ardi Tampu – PlosOne

Bioinformatics

Review: The signal and the noise – characteristics of antisense RNA in complex microbial communities – Thomas Yssing Michaelsen – bioRxiv

SuRF: a New Method for Sparse Variable Selection, with Application in Microbiome Data Analysis – Lihui Liu – arXiv

September 20, 2019

Have a nice day! In this digest, an interesting study about the relationship between peripheral serotonin synthesis and host glucose homeostasis, as well as another study showing the long-term maintained high levels of Proteobacteria in Crohn’s disease. And, of course, more papers!

 

Human and General Microbiome

Are we Ready for a “Microbiome-Guided Behaviour” Approach? – Andrea Lavazza – Cambridge Quarterly of Healthcare Ethics

The gut microbiome regulates host glucose homeostasis via peripheral serotonin – Alyce M. Martin – PNAS

Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis – M. K. Vester-Andersen – Scientific Reports

The Gut Microbiome and Pediatric Cancer: Current Research and Gaps in Knowledge – Roma Bhuta – JNCI Monographs

Time to test antibacterial therapy in Alzheimer’s disease – Francesco Panza – Brain

Discrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities – Qiang Zeng – Scientific Reports

Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples – Sonia Tarallo – mSystems

Analysis of gut microbiome, nutrition and immune status in autism spectrum disorder: a case-control study in Ecuador – María Fernanda Zurita – Gut Microbes 

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – BJOG

Development of an Index Score for Intestinal Inflammation-Associated Dysbiosis Using Real-World Stool Test Results – Lihong Chen – Digestive Diseases and Sciences

Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome – Carrie E. Jung – Scientific Reports

Dysbiotic microbiota in autistic children and their mothers: persistence of fungal and bacterial wall-deficient L-form variants in blood – N. Markova – Scientific Reports

Features of Fecal and Colon Microbiomes Associate With Responses to Biologic Therapies for Inflammatory Bowel Diseases: a Systematic Review – Maria Manuela Estevinho – Clinical Gastroenterology and Hepatology

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients – Anuradha Ravi – Microbial Genomics

Complex interactions between the microbiome and cancer immune therapy – Drew J. Schwartz – Critical Reviews in Clinical Laboratory Sciences

Disentangling the effect of host genetics and gut microbiota on resistance to an intestinal parasite – Bruno Faivre – International Journal for Parasitology

Small talk: microbial metabolites involved in the signaling from microbiota to brain – Giorgia Caspani – Current Opinion in Pharmacology

Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients – Solveig Tangedal – PLoS One

 

Animal Microbiome / Animal Experiments

Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster – Seth M. Rudman – PNAS

Abnormal composition of gut microbiota is associated with resilience versus susceptibility to inescapable electric stress – Kai Zhang – Translational Psychiatry

Adenovirus infection is associated with altered gut microbial communities in a non-human primate – Wasimuddin – Scientific Reports

 

Beneficial Microbes and Compounds

Honey Polyphenols Ameliorate DSS-induced Ulcerative Colitis Via Modulating Gut Microbiota in Rats – Haoan Zhao – Molecular Nutrition and Food Research

ω-3 PUFAs Alleviate High-fat Diet Induced Circadian Intestinal Microbes Dysbiosis – Lifeng Gui – Molecular Nutrition and Food Research

Additional Candida albicans administration enhances the severity of dextran sulfate solution induced colitis mouse model through leaky gut-enhanced systemic inflammation and gut-dysbiosis but attenuated by Lactobacillus rhamnosus L34 – Wimonrat Panpetch – Gut Microbes

Equol: A Bacterial Metabolite from The Daidzein Isoflavone and Its Presumed Beneficial Health Effects –  Baltasar Mayo – Nutrients

Dietary cranberry suppressed colonic inflammation and alleviated gut microbiota dysbiosis in dextran sodium sulfate-treated mice – Xiaokun Cai – Food and Function

 

Food Microbiome

Deciphering the microbiome shift during fermentation of medicinal plants – Martina Köberl – Scientific Reports

 

Plant Microbiome

The aeroponic rhizosphere microbiome: community dynamics in early succession suggest strong selectional forces – Jennifer W. Edmonds – Antonie van Leeuwenhoek

 

Extremophiles

A shared core microbiome in soda lakes separated by large distances – Jackie K. Zorz – Nature Communications

 

Methods

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method – Sukithar K. Rajan – PLoS One

Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing – Emma E. Ilett – Scientific Reports

 

September 17, 2019

Happy Tuesday! Today’s digest includes wastewater treatment biofilms, the microbiome during Crohn’s disease remission, and the bacteria associated with acid mine drainage. Enjoy!

Human oral microbiome

Succession of oral microbiota community as a tool to estimate postmortem interval – Dong – Scientific Reports

Human gut microbiome

Remission in Crohn’s disease is accompanied by alterations in the gut microbiota and mucins production – Magro – Scientific Reports

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation – Ingham – Microbiome

Effect of a Chinese medical nutrition therapy diet on gut microbiota and short chain fatty acids in the simulator of the human intestinal microbial ecosystem (SHIME) – Wu – Journal of Functional Foods

A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals – Scepanovic – Microbiome

Animal experiments

Dietary Bovine Milk Exosomes Elicit Changes in Bacterial Communities in C57BL/6 Mice – Zhou – American Journal of Physiology

Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome – Cabral – Cell Metabolism

Animal microbiome

Maternal vs artificial rearing shapes the rumen microbiome having minor long‐term physiological implications – Belanche – Environmental Microbiology

Plant, root, and soil microbiome

Impact of continuous Panax notoginseng plantation on soil microbial and biochemical properties – Zhang – Scientific Reports

Three Bermudagrass-suppression techniques have little effect on soil-nutrient availability and microbial communities 200 days after application – Farthing – Applied Soil Ecology

Water and extremophile microbiome

Effect of salinity on mature wastewater treatment biofilm microbial community assembly and metabolite characteristics – Wang – Science of the Total Environment

Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis – Lukhele – Extremophiles

Abiotic stress resistance, plant growth promotion and antifungal potential of halotolerant bacteria from a Tunisian solar saltern – Masmoudi – Microbiological Research

Built environment

Effective removal of antibiotic resistance genes and potential links with archaeal communities during vacuum-type composting and positive-pressure composting – Fan – Journal of Environmental Science

Hydraulically Fractured Natural-Gas Well Microbial Communities Contain Genomic Halogenation and Dehalogenation Potential – Evans – Environmental Science & Technology Letters

Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks rapid sand filters – Harder – FEMS Microbiology Ecology