July 8, 2018

Today’s Microbiome Digest blog comes up with the current research articles on the microbiome of GIT, Respiratory, UT, Vagina, Infant, Oral, Marine, Plant-Soil and Animal- Bird. It also features the articles on the bioremediation, pre/pro-biotics, nutrient and dietary effects on microbiome, the potential prognosis, biofilm reduction and multi-omics study of pregnancy cohort, role of Environmental Contaminants(ECs), spore-forming bacteria, attenuation of colitis score, systematic repercussions by antibiotics, glucocorticoid signaling, TMAO, drug-induced liver injury (DILI), neurotransmitter interactions, effect of glycation of fish proteins, NOD2-IBD, Carbapenemase-producing Enterobacteriaceae (CPE).

Have a look and enjoy SUNDAY!

EVENTS, JOBS, PhD POSITIONS:

EVENT – Third Annual Microbiome Symposium on September 24 , 8:00AM – 7:00PM at the Stanford Faculty Club

 

GASTRO-INTESTINAL MICROBIOME: 

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas – Bhabatosh Das – Scientific Reports 

Review – The Mammalian Intestinal Microbiome: Composition, Interaction with the Immune System, Significance for Vaccine Efficacy, and Potential for Disease Therapy – Desselberger U – Pathogens

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients – Bahtiyar Yilmaz – PLoS One

Absence of NOD2 receptor predisposes to intestinal inflammation by a deregulation in the immune response in hosts that are unable to control gut dysbiosis – Patrícia Reisde Souza – Immunobiology

Review – Outside the liver box: The gut microbiota as pivotal modulator of liver diseases – Annika Wahlström – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

 

RESPIRATORY MICROBIOME:

Review – Microbiome in the primary prevention of allergic diseases and bronchial asthma – B.Sozańska – Allergologia et Immunopathologia

Severe Obstructive Sleep Apnea is Associated with Alterations in the Nasal Microbiome and Increase in Inflammation – Benjamin G Wu – American Journal of Respiratory and Critical Care Medicine

URINARY TRACT MICROBIOME:

Review – Infections – The Urinary Tract Microbiome: The Answer to All Our Open Questions? – Giuseppe Magistro – European Urology focus

VAGINAL MICROBIOME:

Anti-HIV-1 Activity of Lactic Acid in Human Cervicovaginal Fluid – Tyssen D – mSphere

INFANT MICROBIOME:

Bifidobacterium longum subsp. infantis EVC001 stably restores the infant gut microbiome over the first year of life in breastfed infants – Jennifer Smilowitz – Pediatrics

Review – Does antibiotic choice for the treatment of suspected late-onset sepsis in premature infants determine the risk of developing necrotising enterocolitis? A systematic review – Josephine V.Seale – Early Human Developmment

ORAL MICROBIOME: 

Review – Cariogenic microbiome and microbiota of the early primary dentition: a contemporary overview – Fakhruddin KS – Oral Diseases

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin – Mann AE – Scientific Reports

Distinctions and associations between the microbiota of saliva and supragingival plaque of permanent and deciduous teeth – Shi W – PLoS One

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease – Kazumichi Abe – PLoS One

GENERAL HUMAN MICROBIOME:

Human-associated microbial populations as evidence in forensic casework – Frederike C.A – Forensic Science International: Genetics

Book chapter – Genomics and Drug-Metabolizing Enzymes and Its Application in Drug Delivery: Evaluating the Influence of the Microbiome – Sheeba Varghese Gupta

Effects of Substance Use and Sex Practices on the Intestinal Microbiome During HIV-1 Infection – Jennifer A Fulcher –The Journal of Infectious Diseases

Preview – Interactions between Clostridioides difficile and fecal microbiota in in vitro batch model: growth, sporulation and microbiota changes – Sabina Horvat – Frontiers in Microbiology

Review – Metagenomic and clinical microbiology – Sophie Amrane – Human Microbiome

Implants induce a new niche for microbiomes – Tim H. Jakobsen – Wiley Online Library

Short Communication Transmission of IMI-2 carbapenemase-producing Enterobacteriaceae from river water to human – Chrislène Laurens – Journal of Global Antimicrobial Resistance

Review – The hygiene hypothesis: immunological mechanisms of airway tolerance – Eline Haspeslagh – Current Opinion in Immunology

Microbiota affects the expression of genes involved in HPA axis regulation and local metabolism of glucocorticoids in chronic psychosocial stress – M. Vodička – Brain, Behavior, and Immunity

Review – The Role of Microbiota in Cardiovascular Risk: Focus on Trimethylamine Oxide – HusseinAl-Rubaye – Current Problems in Cardiology

 

HUMAN-MICROBE CROSS-TALK:

Gut Microbiota-Dependent Trimethylamine N-Oxide Predicts Risk of Cardiovascular Events in Patients With Stroke and Is Related to Proinflammatory Monocytes – Haghikia A – Arterioscler Thromb Vasc Biol.

Cutting Edge: Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism – Catherine R. Lammert – J Immunol

Critical Role for the Microbiota in CX3CR1+ Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses – Myunghoo Kim – Immunity

 

MARINE/WATER MICROBIAL ECOLOGY:

Review – Ecology and evolution of seafloor and subseafloor microbial communities – WD Orsi – Nature Reviews Microbiology

Metabolic potential of microbial communities from ferruginous sediments – Aurèle Vuillemin – Environmental Microbiology

Metagenomic analysis of basal ice from an Alaskan glacier – Kayani MUR – Microbiome

Patterns of Change in Metabolic Capabilities of Sediment Microbial Communities in River and Lake Ecosystems – Oest A1 – Int J Microbiol

Succession of toxicity and microbiota in hydraulic fracturing flowback and produced water in the Denver–Julesburg Basin – Natalie M Hull – Science of The Total Environment

 

PLANT or SOIL MICROBIOME:

Preview – New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes – Marie E. Kroeger – Frontiers in Microbiology

Litter quality drives the differentiation of microbial communities in the litter horizon across an alpine treeline ecotone in the eastern Tibetan Plateau – Haifeng Zheng – Scientific Reports

Preview – Unravelling the composition of the root-associated bacterial microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology

 

BIOREMEDIATION:

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor – Nsanzumukiza Martin Vincent – Int. J. Environ. Res. Public Health

Review – Response of microbial communities to oil spill in the Gulf of Mexico: A review – Linda Adzigbli – Afr. J. Microbiol. Res

A two-staged system to generate electricity in microbial fuel cells using methane – Jaewook Myung – Chemical Engineering Journal

The influence of pressure on crude oil biodegradation in shallow and deep Gulf of Mexico sediments – Nguyen UT – PLoS One

Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers – Robert E. Danczak – mSystems

Energy efficiency: Importance of indigenous microorganisms contained in the municipal solid wastes – S.Zahedi – Waste management

Systematic characterization and proposed pathway of tetracycline degradation in solid waste treatment by Hermetia illucens with intestinal microbiota – Minmin Cai – Environmental Pollution

 

NUTRITION or DIET and TREATMENTS:

Functional Effects of the Buckwheat Iminosugar d-Fagomine on Rats with Diet-Induced Prediabetes – Ramos-Romero S – Mol Nutr Food Res

Long-Term Genistein Consumption Modifies Gut Microbiota, Improving Glucose Metabolism, Metabolic Endotoxaemia and Cognitive Function in Mice Fed a High-Fat Diet – López P – Mol Nutr Food Res

Brown rice-specific γ-oryzanol as a promising prophylactic avenue to protect against diabetes mellitus and obesity disease in humans – Masuzaki H – J Diabetes Investig

Intestinal Inflammation in Chilean Infants Fed With Bovine Formula vs. Breast Milk and Its Association With Their Gut Microbiota – Ossa JC – Front Cell Infect Microbiol.

Trigonelline inhibits intestinal microbial metabolism of choline and its associated cardiovascular risk – Anwar S – J Pharm Biomed Anal

Off-target effects of tribendimidine, tribendimidine plus ivermectin, tribendimidine plus oxantel-pamoate, and albendazole plus oxantel-pamoate on the human gut microbiota – Pierre H.H.Schneeberger – International Journal for Parasitology: Drugs and Drug Resistance

Isoquercetin and inulin synergistically modulate the gut microbiome to prevent development of the metabolic syndrome in mice fed a high fat diet – Si Tan – Scientific Reports

Glycation of fish protein impacts its fermentation metabolites and gut microbiota during in vitro human colonic fermentation – Yuhong Yang – Food Research International

Correlation between microbiota and flavours in fermentation of Chinese Sichuan Paocai – YangshengXiao – Food Research International

Review – Relationship between fatty acids intake and Clostridium coccoides in obese individuals with metabolic syndrome – Giovana Jamar – Food Research International

Review – Microbiota of milk powders and the heat resistance and spoilage potential of aerobic spore-forming bacteria – Faizan A.Sadiq – International Diary Journal

Review – The debate over neurotransmitter interaction in aspartame usage – Arbind Kumar Choudhary – Journal of Clinical Neuroscience

 

METHODS:

Reevaluating approaches to cystic fibrosis pulmonary exacerbations – Schechter MS – Pediatr Pulmonol

Review – Bioresponsive drug delivery systems in intestinal inflammation: State-of-the-art and future perspectives – Niranjan G.Kotla – Advance Drug Delivery Reviews

Rapid analysis of photoautotroph microbial communities in soils by flow cytometric barcoding and fingerprinting – László Menyhárt – Applied Soil Ecology

Degradation studies of modified inulin as potential encapsulation material for colon targeting and release of mesalamine – MichaelWalz – Carbohydrate Polymers

Review – Advances in drug-induced cholestasis: Clinical perspectives, potential mechanisms and in vitro systems – M. LeonorFernández-Murga – Food and Chemical Toxicology

 

ANIMAL and BIRD MICROBIOME:

Characteristics of microbial communities and intestinal pathogenic bacteria for migrated Larus ridibundus in southwest China – Liao F – Microbiology Open

Gut microbiota correlates with fiber and apparent nutrients digestion in goose – Guojun Liu – Poultry Science

Feeding sows resistant starch during gestation and lactation impacts their faecal microbiota and milk composition but shows limited effects on their progeny – Julie Leblois – PLoS One

Analysis of temporal fecal microbiota dynamics in weaner pigs with and without exposure to enterotoxigenic Escherichia coli – J. Pollock – Journal of Animal Science

 

ANIMAL EXPERIMENTS:

Aryl hydrocarbon receptor/IL-22/Stat3 signaling pathway is involved in the modulation of intestinal mucosa antimicrobial molecules by commensal microbiota in mice – Wang J – Innate Immun.

Oral infection of mice with Fusobacterium nucleatum results in macrophage recruitment to the dental pulp and bone resorption – Larry Johnson – Biomedical Journal

Preview – Fecal Microbiota Transplantation is Associated with Reduced Morbidity and Mortality in Porcine Circovirus Associated Disease – Megan C. Niederwerder – Frontiers in Microbiology

Oral treatment with Lactobacillus rhamnosus 64 during the early postnatal period improves the health of adult rats with TNBS-induced colitis – Stanislava Stanojević – Journal of Functional Foods

Antibiotic-induced dysbiosis effects on the murine gastrointestinal tract and their systemic repercussions – Caio PupinRosa – Life Sciences

 

MICROBIOLOGY:

N-Acetyl-glucosamine influences the biofilm formation of Escherichia coli – Sicard JF – Gut Pathog

Benzoyl Peroxide Inhibits Quorum Sensing and Biofilm Formation by Gardnerella vaginalis 14018 – Ammar Algburi – Infectious Diseases in Obstetrics and Gynecology

 

PRE/PRO – BIOTICS:

Review : Benefaction of probiotics for human health: A review – George Kerry R – J Food Drug Anal

Review – Role of prebiotics in regulation of microbiota and prevention of obesity – Grethel T.Choque Delgado – Food Research International

Effects of the Administration of Probiotics on Fecal Microbiota Diversity and Composition in Healthy Individuals – Choong-Kyun Noh – J Neurogastroenterol Motil

 

METABOLOMICS:

Microbiome-related metabolite changes in gut tissue, cecum content and feces of rats treated with antibiotics – C.Behr – Toxicology and Applied Pharmacology

 

MULTI-OMICS PICKS:

Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Human Pregnancy – Mohammad Sajjad Ghaemi – Bioinformatics

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June 26, 2018

Today’s Microbiome Digest cover the topics on bioinformatics; methods and models; trials and therapies; infection and immunity; microbiome of human gut, human vagina, insect, animals, plant, marine; food and nutrition; bioremediation and metabolomics.

 

EVENTS- JOBS – PhD POSITIONS:

Event – Organoids: Modelling Organ Development and Disease in 3D Culture – EMBO| EMBL Symposia

 

NEWS and VIEWS:

Pairing off: a bottom-up approach to the human gut microbiome– Clare Abreu – Molecular Systems Biology

 

BIOINFORMATICS:
Zero-inflated generalized Dirichlet multinomial regression model for microbiome compositional data analysis – Tang ZZ – Biostatistics

 

METHODS and MODELS:

Book Chapter – Methods for Microbiota Analysis: Sample Collection and Laboratory Methods – Saleh Ibrahim – The Microbiome in Rheumatic Diseases and Infection

Review: Culturing the human microbiota and culturomics – Lagier JC – Nature Reviews Microbiology

Using glycolysis enzyme sequences to inform Lactobacillus phylogeny – Katelyn Brandt – Microbial Genomics

Multicenter study establishing the clinical validity of a nucleic-acid amplification-based assay for the diagnosis of bacterial vaginosis – Cartwright CP – Diagnostics Microbiology and Infectious Disease.

PATENT – SYSTEM AND METHODS FOR DEVELOPING AND USING A MICROBIOME-BASED ACTION COMPONENT FOR PATIENT HEALTH – Warren Tracy, Jantzen Tammi Gregory Katherine

 

TRIALS and THERAPIES:

Antimicrobial photodynamic therapy as a new approach for the treatment of vulvovaginal candidiasis: preliminary results – Aline Silva Sousa – Lasers in Medical Science

Review – Prevention of Cystitis: Travelling between the Imaginary and Reality – Vecchio M – Annals of Nutrition and Metabolism

 

INFECTIONS and IMMUNITY:

Book Chapter – The Impact of Infections on Reproduction and Fertility – VE Jones – Clinical Reproductive Science

Intestinal barrier disruption and dysregulated mucosal immunity contribute to kidney fibrosis in chronic kidney disease – Yang J – Nephrology Dialysis Transplantation

In Press: Treatment and Prevention of Recurrent Lower Urinary Tract Infections in Women: A Rapid Review with Practice Recommendations – Ariana l Smith – The Journal of Urology

Book Chapter – Immunology of the Microbiome: Implications for Rheumatoid Arthritis and Other Autoimmune Diseases – Daniel M Altmann – The Microbiome in Rheumatic Diseases and Infection

 

VAGINAL MICROBIOME:

Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov. – Diop K – Microbiology Open

 

GUT MICROBIOME: 

Preview – Gut microbiota as a missing link between nutrients and traits of human – Hea-Jong Chung – Frontiers in Microbiology

Preview – The gut-brain axis, the human gut microbiota and their integration in the development of obesity – Edward S Bliss – Frontiers in Microbiology

Review – The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes – Ömrüm Aydin – Current Diabetes reports

Beneficial metabolic effects of 2’, 3’, 5’-tri-acetyl-N6-(3-hydroxylaniline) adenosine in multiple biological matrices and intestinal flora of hyperlipidemic hamsters– Tianqi Li – Journal of Proteome Research

 

ANIMAL MICROBIOME:

Preview – Dynamics of gut microbiota diversity during the early development of an avian host: evidence from a cross-foster experiment – Aimeric Teyssier – Frontiers in Microbiology

Enterococcus faecium WEFA23 from infant lessens high-fat-diet-induced hyperlipidemia via cholesterol 7-alpha-hydroxylase gene by altering the composition of gut microbiota in rats – Fuqing Huang – ScienceDirect

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs – Flancman R – PloS One

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing – Ramesh J Pandit – Microbiome

 

GENERAL MICROBIOME:

Review – Role of nutrition, infection, and the microbiota in the efficacy of oral vaccines – Amrita Bhattacharjee – Clinical Science

Commensal Microbiota Enhance Both Osteoclast and Osteoblast Activities – Yoko Uchida – Molecules

 

PLANT/ROOT/SOIL MICROBIOME:

Editorial – The contribution of plant microbiota to economy growth – Angela Sessitsch – Microbial Biotechnology

Colonization cues of leaf- and root-inhabiting bacterial microbiota of Atractylodes lancea derived in vitro and in vivo – Yong Jia – Plant and Soil

Preview – Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism – Yuanchan Luo – – Frontiers in Microbiology

Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a HighSalinity Environment – Juan Ignacio Vílchez – GenomeAnnouncements

 

INSECT MICROBIOME:

Exposure of soil collembolans to microplastics perturbs their gut microbiota and alters their isotopic composition – DongZhu – Soil Biology and Biochemistry

 

SKIN MICROBIOME:

Book Chapter – Psoriasis and Psoriatic Arthritis – Madhura Castelino – The Microbiome in Rheumatic Diseases and Infection

 

MARINE MICROBIOME:
Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses – Felipe Hernandes Coutinho – Trends in Microbiology

 

NEONATAL/INFANT MICROBIOME:

Communication – Maternal Intrapartum Antibiotic Administration and Infantile Colic: Is there a Connection? – Leppälehto E – Neonatology

Review – Intrauterine Inflammation, Epigenetics, and Microbiome Influences on Preterm Infant Health – Lu L – Current Pathobiology Reports

 

CROSS – POPULATION MICROBIOME:
Similarities and differences in gut microbiome composition correlate with dietary patterns of Indian and Chinese adults – Abhishek Jain – AMB Express

 

PHAGES/VIRUSES:

Genome Sequence of the Pseudomonas protegens Phage GP100 – Jordan Vacheron – GenomeAnnouncements

 

FOOD and NUTRITION:

Plasma and urine metabolite profiling reveals the protective effect of Clinacanthus nutans in an ovalbumin-induced anaphylaxis model: 1H-NMR metabolomics approach – Leng Wei Khoo – Journal of Pharmaceutical and Biomedical Analysis

Drivers that establish and assembly the lactic acid bacteria biota in cheeses – Marco Gobbetti – Trends in Food Science & Technology

The food safety of DP-356Ø43 soybeans on SD rats reflected by physiological variables and fecal microbiota during a 90-day feeding study – Zou S – Regul Toxicol Pharmacol

Fermented Soybean Suppresses Visceral Fat Accumulation in Mice – Kushida M – Molecular Nutrition and Food Research

Combined Use of C. butyricum Sx-01 and L. salivarius C-1-3 Improves Intestinal Health and Reduces the Amount of Lipids in Serum via Modulation of Gut Microbiota in Mice – Long M – Nutrients

Review – Dietary polyphenols: A novel strategy to modulate microbiota-gut-brain axis – Diana Serra – Trends in Food Science & Technology

 

METABOLOMICS:

Non-invasive urinary metabolomic profiles discriminate biliary atresia from infantile hepatitis syndrome – Wei-Wei Li – Metabolomics

Metabolomics of the amniotic fluid: Is it a feasible approach to evaluate the safety of Chinese medicine during pregnancy? – Jinjun Shan – Journal of Applied Toxicology

Article – A validated, fast method for quantification of sterols and gut microbiome derived 5α/β-stanols in human faeces by isotope dilution LC-high resolution MS – Schoett HF – Analytical Chemistry

 

BIOREMEDIATION:

Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing – Mariela Beatriz Reyes-Sosa – Science of The Total Environment

 

ANTIBIOTIC SUSCEPTIBILITY:
Skin and nasal vestibule colonisation by Staphylococcus aureus and its susceptibility to drugs in atopic dermatitis patients – Wrobel J – Annals of Agriculture and Environmental Medicine