Author Archives: ojasvi

December 30, 2018

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In the midst of the festive season have a fiesta with the recent articles on Microbiome. Todays MicroBiome Digest covers the Techniques and Treatments, Drugs, Immunostimulatory Diet and Nutrition, Multivariate Count Data Model, Antimicrobials, Pre/Pro-biotcs, Host-Microbe Interactions, Genes, Genomics and Pathways of Microbiota, Infant Microbiome, Animal Models, Animal Microbiome, Microbial Ecology of plant and soil. Happy Reading!!! 

TECHNIQUES & TREATMENTS:

LEMMI: A Live Evaluation of Computational Methods for Metagenome Investigation – Mathieu Seppey – bioRxiv

Single-cell virus sequencing of influenza infections that trigger innate immunity – Alistair B Russell – bioRxiv

METHODS TO IMPROVE INDUCTION OF IGG AND IGA ANTIBODIES BY VACCINES – Boyaka, Prosper -United States Patent Application 20180360953 -PATENT

Are the Statins promising antifungal agents against invasive candidiasis? – William GustavoLima -Biomedicine & Pharmacotherapy

Bayesian variable selection for multivariate zero-inflated models: Application to microbiome count data – Lee KH – Biostatistics

Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing – Mu DS – Microbiome

Prognostic Impact of Fusobacterium nucleatum Depends on Combined Tumor Location and Microsatellite Instability Status in Stage II/III Colorectal Cancers Treated with Adjuvant Chemotherapy – Oh HJ – J Pathol Transl Med.

Loss of Gut Microbiota Alters Immune System Composition and Cripples Post-Infarction Cardiac Repair – Tang TW – Circulation

DRUG, DIET and NUTRITION:

Review article: implementation of a diet low in FODMAPs for patients with irritable bowel syndrome-directions for future research – Mitchell Hrticle – Aliment Pharmacol Ther.

Compound polysaccharides ameliorate experimental colitis by modulating gut microbiota composition and function – Cai Y – J Gastroenterol Hepatol.

Rifaximin Altered Gut Microbiota Components Associated with Liver/Neuropsychological Functions in Patients with Hepatic Encephalopathy: An Exploratory Data Analysis of a Phase II/III Clinical Trials – Kawaguchi T – Hepatol Res.

Inulin ameliorates alcoholic liver disease via suppressing LPS-TLR4-Mψ axis and modulating gut microbiota in mice – Yang X – Alcohol Clin Exp Res.

Effect of Resistant Starch on the Gut Microbiota and Its Metabolites in Patients with Coronary Artery Disease – Yoshida N – J Atheroscler Thromb.

Late gestation diet supplementation of resin acid-enriched composition increases sow colostrum immunoglobulin G content, piglet colostrum intake and improve sow gut microbiota – Hasan S – Animal

PRE/PRO- BIOTICS and ANTIMICROBIAL:

The human skin microbiota is a rich source of bacteriocin producing staphylococci which kill human pathogens – O’Sullivan JN – FEMS Microbiol Ecol.

Comparative immunostimulatory effect of probiotics and prebiotics in Channa punctatus against Aphanomyces invadans – Devi G – Fish Shellfish Immunol

GENES, GENOMICS & PATHWAYS:

Detection of a novel mutation G511T in the 530 loop in 16S rRNA in multi drugs resistant Mycobacterium tuberculosis isolated from Sudanese patients – Yousif Mohammed Alfatih – bioRxiv

Review: Interactions Between Autophagy and the Unfolded Protein Response: Implications for Inflammatory Bowel Disease – Hooper KM – Inflamm Bowel Dis.

In vitro and in vivo characterization of Clostridium scindens bile acid transformations – Marion S- Gut Microbes

Bioinformatic, phylogenetic, and chemical analysis of the UV-absorbing compounds scytonemin and mycosporine-like amino acids from the microbial mat communities of Shark Bay, Australia – D’Agostino PM – Environ Microbiol

Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses – Tyakht AV – BMC Genomics

Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan – Sekizuka T – mSphere

HOST-MICROBE INTERACTION:

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles – Antoine P Pagé -bioRxiv

Bacterial secretion of histamine within the gut influences immune responses within the lung – Barcik W – Allergy

GUT MICROBIOME:

Extensive Transmission of Microbes along the Gastrointestinal Tract – Thomas SB Schmidt – bioRxiv

VAGINAL MICROBIOME:

Human β-defensin-2 as a biochemical indicator of vaginal environment in pregnant women – Hideko Kotani – Hypertension Research In Pregnancy

PREGNANCY AND EARLY LIFE:

Physiology of Stress and Use of Skin-to-Skin Care as a Stress-Reducing Intervention in the NICU – Britt Frisk Pados – Nursing for Women’s Health

Longitudinal analysis of infant stool bacteria communities before and after acute febrile malaria and artemether/lumefantrine treatment – Mandal RK – J Infect Dis.

Haemophilus-dominant nasopharyngeal microbiota is associated with delayed clearance of respiratory syncytial virus in infants hospitalized for bronchiolitis – Mansbach JM – J Infect Dis

ANIMAL MODEL EXPERIMENTS:

Dietary nucleotides can directly stimulate the immunity of zebrafish independent of the intestinal microbiota – Guo X – Fish Shellfish Immunol.

Antimicrobial assessment of phage therapy using a porcine model of biofilm infection – Milho C – Int J Pharm

ANIMAL MICROBIOME:

Effect of different levels of tryptophan on productive performance, egg quality, blood biochemistry, and caecal microbiota of hens housed in enriched colony cages under commercial stocking density – Khattak F -Poult Sci.

Exogenous carbohydrases added to a starter diet reduced markers of systemic immune activation and decreased Lactobacillus in weaned pigs – Li Q – J Anim Sci.

Gut microbiota dynamics and functionality in Reticulitermes grassei after a 7-day dietary shift and ciprofloxacin treatment – Berlanga M – PLoS One

MICROBIAL ECOLOGY:

Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia – Yasir M – OMICS

Rhizosphere microorganisms can influence the timing of plant flowering – Lut T – Microbiome

December 16, 2018

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A Happy Weekend to one and all. 

Today’s Microbiome Digest features the recent articles covering the techniques and treatments, microbiome of infants, gut, oral, eye and vaginal microbiome, host-microbe interactions, diet and probiotic supplementations, co-culture models and its impact on biofilm reduction, soil microbiome and microbial ecology, comparative study of microbiome in various diseases, role of microbiome on various cancers, metabolomics, animal and insect microbiome, myco and yeast biome, genes and genomics of good and bad bacteria.  ENJOY READING.

TECHNIQUES:

Rapid Determination of Antibiotic Susceptibility by Stimulated Raman Scattering Imaging of D2O Metabolism – Weili Hong – bioRxiv

CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR – Matthew G Links – bioRxiv

Characterization of Hydrocarbon-Degrading Bacteria in Constructed Wetland Microcosms Used to Treat Crude Oil Polluted Water– Amer Jamal Hashmat- Bulletin of Environmental Contamination and Toxicology

A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome – Whidbey C – J Am Chem Soc.

Combined extraction method for metabolomic and PLFA analysis of soil – Jeffrey S.Buyer – Applied Soil Ecology

CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes – Andres Benavides – BMC Genomics

Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli – Yong JunGoh – Current Opinion in Biotechnology

Evaluating the Efficiency of Primer Extension Capture as a Method to Enrich DNA Extractions – Winters M – J Forensic Sci

TREATMENTS:

Intestinal Anti-Inflammatory Activity of the Aqueous Extract from Ipomoea asarifolia in DNBS-Induced Colitis in Rats – da Silva VC – Int J Mol Sci.

Effect of Marine Microalga Chlorella pyrenoidosa Ethanol Extract on Lipid Metabolism and Gut Microbiota Composition in High-Fat Diet-Fed Rats – Wan X – Mar Drugs

Flavonoids and Colorectal Cancer Prevention – Li Y – Antioxidants (Basel)

Effects of Rich-Polyphenols Extract of Dendrobium loddigesii on Anti-Diabetic, Anti-Inflammatory, Anti-Oxidant, and Gut Microbiota Modulation in db/db Mice – Li XW – Molecules

Evidence-based mixture containing Lactobacillus strains and lactoferrin to prevent recurrent bacterial vaginosis: a double blind, placebo controlled, randomised clinical trial – R. Russo – Beneficial Microbes

ORAL MICROBIOME:

Bacterial profile of the supragingival dental biofilm in children with deciduous and early mixed dentition using next generation sequencing (HOMINGS) technique – Harris-Ricardo J – Enferm Infecc Microbiol Clin.

Oral Dysbiosis in Pancreatic Cancer and Liver Cirrhosis: A Review of the Literature – Mohammed H – Biomedicines

Subgingival lipid A profile and endotoxin activity in periodontal health and disease – Strachan A – Clin Oral Investig

GENOME AND GENOMICS:
Iron-associated protein interaction networks reveal the key functional modules related to survival and virulence of Pasteurella multocida – Theeraphol Jatuponwiphat – Microbial Pathogenesis

Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis – Reaz Uddin – Microbial pathogenesis

Epilithic Biofilms in Lake Baikal: Screening and Diversity of PKS and NRPS Genes in the Genomes of Heterotrophic Bacteria – Sukhanova E – Pol J Microbiol.

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa – Fitzgerald CB – BMC Genomics

INSECT MICROBIOME:

Metagenomic 16S rRNA gene sequencing survey of Borrelia species in Irish samples of Ixodes ricinus ticks – John S Lambert – bioRxiv

MARINE MICROBIOME:

Uncultured marine cyanophages encode for active NblA, phycobilisome proteolysis adaptor protein – Omer Nadal – bioRxiv

A fundamental difference between macrobiota and microbial eukaryotes: Protistan plankton has a species maximum in the freshwater-marine transition zone of the Baltic Sea – Filker S – Environ Microbiol

ANTIBIOTIC RESISTANCE:

Antibiotic usage promotes the evolution of resistance against gepotidacin, a novel multi-targeting drug – Petra Szili – bioRxiv

Role of Bentonite on the Mobility of Antibiotic Resistance Genes, and Microbial Community in Oxytetracycline and Cadmium Contaminated Soil – Guo H – Front Microbiol

HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance – Duval M – Proc Natl Acad Sci U S A.

Antibiotics may increase triazine herbicide exposure risk via disturbing gut microbiota – Zhan J – Microbiome

SOIL MICROBIOME:

REVIEW: The rhizosphere microbiome: A key component of sustainable cork oak forests in trouble – Fatima Zahra Maghnia – Forest Ecology and Management

VIROME:

The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics – Diane A.Lima – Virus Research

MYCO and YEAST-BIOME:

Snf2 controls pulcherriminic acid biosynthesis and connects pigmentation and antifungal activity of the yeast Metschnikowia pulcherrima – Deborah Gore-Lloyd – bioRxiv

Nitrogen deprivation in Fusarium oxysporum promotes mycotoxin production via intermediates in the Krebs cycle and unreported methylmalonyl-CoA mutase activity – A. V. Karpe – Metabolomics

METABOLOMICS:

Gut microbiome structure and metabolic activity in inflammatory bowel disease – Eric A. Franzosa – Nature Microbiology

Active Acupoints Differ from Inactive Acupoints in Modulating Key Plasmatic Metabolites of Hypertension: A Targeted Metabolomics Study – Yang M – Sci Rep

Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic – Liu CW – J Proteome Res.

GENERAL MICROBIOME:

The Human Microbiome in Health and Disease – Wyatt M. Arnold – Genomic Applications in Pathology

Microbes: possible link between modern lifestyle transition and the rise of metabolic syndrome – Moossavi S – Obes Rev.

CANCER and MICROBIOTA:

Microbiota in cancer development and treatment – Muhammad Hassan Raza – Journal of Cancer Research and Clinical Oncology

Alcohol and gastrointestinal cancers – Vanella G – Curr Opin Gastroenterol.

Gut microbiota in patients after surgical treatment for colorectal cancer – Jin Y – Environ Microbiol

The Microbiome in Bipolar Depression: A Longitudinal Study of One Pair of Monozygotic Twins – Jiang HY – Bipolar Disord.

Gut Microbiota, Fusobacteria, and Colorectal Cancer – Kelly D – Diseases

PRENATAL AND INFANT MICROBIOME:

The Prenatal Microbiome: A New Player for Human Health – D’Argenio V – High Throughput

Enteric dysbiosis and fecal calprotectin expression in premature infants – Thao T. B. Ho – Pediatric Research

Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in human gut. – Oki K – BMC Microbiol.

EYE MICROBIOME:

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye – Jayasudha R – J Biosci.

GUT MICROBIOME:

Gut microbiota dysbiosis in male patients with chronic traumatic complete spinal cord injury – Zhang C – J Transl Med.

Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome – Treangen TJ – Front Immunol.

A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist – Forbes JD – Microbiome.

Microbiome-The Missing Link in the Gut-Brain Axis: Focus on Its Role in Gastrointestinal and Mental Health – Skonieczna-Żydecka K – J Clin Med.

ANIMAL MICROBIOME:

The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism – Fang Liu – Molecular Aurtism

Effects of smoking on the lower respiratory tract microbiome in mice – Zhang R – Respir Res

Evaluating the profound effect of gut microbiome on host appetite in pigs – Yang H – BMC Microbiol.

Comparative analysis of the intestinal bacterial community and expression of gut immunity genes in the Chinese Mitten Crab (Eriocheir sinensis) – Dong J – AMB Express.

Rumen methanogen and protozoal communities of Tibetan sheep and Gansu Alpine Finewool sheep grazing on the Qinghai-Tibetan Plateau, China – Huang J – BMC Microbiol.

PSXIV-15 The Effect Of Intravaginal Progesterone Implant In The Vaginal Microbiota Of Holstein Cows – E Zanella – Journal of Animal Science

The role of the bovine respiratory microbiota in health and disease – T Alexander – Journal of Animal Science

MICROBIAL ECOLOGY:

Polychaete mucopolysaccharide alters sediment microbial diversity and stimulates ammonia-oxidising functional groups – Dale H – FEMS Microbiol Ecol.

Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding – Morales-Cruz A – BMC Microbiol.

The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems – Zhang G – Microbiome

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages – Jacquiod S – Microbiome

Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation – Dai D – Front Microbiol

HOST-MICROBE CROSSTALK:

Neutrophils Restrict Tumor-Associated Microbiota to Reduce Growth and Invasion of Colon Tumors in Mice – Triner D – Gastroenterology

Impact of CFTR modulation with Ivacaftor on Gut Microbiota and Intestinal Inflammation– Ooi CY – Sci Rep

Using Enteric Pathogens to Probe the Gut Microbiota – Spiga L – Trends Microbiol.

DIET, NUTRITION AND PROBIOTICS:

Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition – Svolos V – Gastroenterology

The Dietary Intervention of Transgenic Low-Gliadin Wheat Bread in Patients with Non-Celiac Gluten Sensitivity (NCGS) Showed No Differences with Gluten Free Diet (GFD) but Provides Better Gut Microbiota Profile – Haro C – Nutrients.

SIRT3 Deficiency Promotes High-Fat Diet-Induced Non-Alcoholic Fatty Liver Disease In Correlation With Impaired Intestinal Permeability Through Gut Microbial Dysbiosis – Chen M – Mol Nutr Food Res

Maternal probiotic supplementation for prevention of morbidity and mortality in preterm infants – Grev J – Cochrane Database Syst Rev

Role of prebiotics and probiotics in the functionality of the microbiota in the patients receiving enteral nutrition – Ballesteros Pomar – Nutr Hosp.

Probiotics Streptococcus salivarius 24SMB and Streptococcus oralis 89a interfere with biofilm formation of pathogens of the upper respiratory tract – Bidossi A – BMC Infect Dis

VAGINAL MICROBIOME:

Vaginal dysbiosis, and the risk of human papillomavirus and cervical cancer: systematic review and meta-analysis – Brusselaers N – Am J Obstet Gynecol.

Microbiota dysbiosis is associated with HPV-induced cervical carcinogenesis – Kwasniewski W – Oncol Lett.

CO-CULTURE MODEL and EFFECTS:

Dynamics of Biofilm Formation by Salmonella Typhimurium and Beef Processing Plant Bacteria in Mono- and Dual-Species Cultures – Visvalingam J – Microb Ecol

Anaerobic Degradation of the Plant Sugar Sulfoquinovose Concomitant With H2S Production: Escherichia coli K-12 and Desulfovibrio sp. Strain DF1 as Co-culture Model – Burrichter A – Front Microbiol.

October 23, 2018

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Here comes today’s Microbiome Digest featuring the recent articles on microbial methane oxidizers, sulfidic waters, PM exposure effect on airway microbiome, dysbiotic state of spring fever, diets targeting microbiome and be a cure, peri-implantitis, effect of age and inflammation on mice microbiome, diet effect on monkeys microbiome, fecal microbial transplant in UC patients, cervical microbiome, functional repertoire of ETEC and Bifidobacterium, bile duct inflammation causing microbes, role of probiotics. HAPPY READING.

EVENTS, JOBS, SCHOLARSHIPS:

Commonwealth PhD Scholarships – Study at UK University

ENVIRONMENTAL MICROBIOME:

Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers – He Z – Environ Pollut

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters – Deja-Sikora E – Microb Ecol

HUMAN RESPIRATORY MICROBIOME:

Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure – Wang L – Ecotoxicol Environ Saf

ORAL MICROBIOME:

Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children – Chen B – Int Immunopharmacol

The Severity of Human Peri-Implantitis Lesions Correlates with the Level of Submucosal Microbial Dysbiosis – Kröger A – J Clin Periodontol

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis – Boyer E – Sci Rep

Effects of antimicrobial peptide GH12 on the cariogenic properties and composition of a cariogenic multispecies biofilm – Jiang W – Appl Environ Microbiol
GUT MICROBIOME:

Review: Natural polysaccharides exhibit anti-tumor activity by targeting gut microbiota – Liu L – Int J Biol Macromol

Polysaccharides from Laminaria japonica alleviated metabolic syndrome in BALB/c mice by normalizing the gut microbiota – Duan M – Int J Biol Macromol.

Gut microbiota translocation promotes autoimmune cholangitis – Ma HD – J Autoimmun

Competitive lottery-based assembly of selected clades in the human gut microbiome – Verster AJ- Microbiome

Mini-Review : Leaky Gut, Leaky Brain? – Obrenovich MEM – Microorganisms

REPRODUCTIVE MICROBIOME:

Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study – Arokiyaraj S –
Sci Rep

ANIMAL MODEL MICROBIOME:

Long-term intake of Lactobacillus paracasei KW3110 prevents age-related chronic inflammation and retinal cell loss in physiologically aged mice – Morita Y – Aging

Targeted Diet Modification Reduces Multiple Sclerosis-like Disease in Adult Marmoset Monkeys from an Outbred Colony – Kap YS – J Immuno

FUNCTIONAL REPERTOIRE INSIGHTS:

Cell surface polysaccharides of Bifidobacterium bifidum induce the generation of Foxp3+ regulatory T cells – Verma R – Sci Immunol.

De-O-Acetylation of mucin-derived sialic acids by recombinant NanS-p esterases of Escherichia coli O157:H7 strain EDL933 – Feuerbaum S – Int J Med Microbiol.

PLANT MICROBIOME:

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales – Li HY- Microbiome

METHODS:

Protocol for faecal microbiota transplantation in ulcerative colitis (FMTUC): a randomised feasibility study – Jitsumura M – BMJ Open

PROBIOTICS:

Probiotics in Autoimmune and Inflammatory Disorders – Liu Y – Nutrients

NON-MICROBIOME PICK:

Preprint: Segregational drift and the interplay between plasmid copy number and evolvability – Judith Ilhan- Biorxiv

October 3, 2018

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Enjoy Reading today’s Microbiome Digest blog focusing on the research articles covering the techniques, what and how treatments alter the microbiome, potential of mycobiome to produce fuels and chemicals, pathogenic functions, gut microbiome, animal microbiome, soil microbiome, Maternal Immune Activation(MIA) and its effect and probiotics from vaginal microbiome. 

TECHNIQUES:

Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host–Microbiota Interactions – Pranjul Shah – Microbial Proteomics

A primer on investigating the role of the microbiome in brain and cognitive development – Caroline Kelsey – Developmental Psychobiology

TREATMENTS:

Roux-Y Gastric Bypass and Sleeve Gastrectomy directly change gut microbiota composition independent of operation type – Fernanda L. Paganelli – bioRxiv

Review – Systematic review on the first line treatment of amphotericin B in critically ill adults with candidemia or invasive candidiasis – Sean Keane – Expert Review of Anti-infective Therapy

Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant – Ying Taur – Gut Microbiota

Review – Reciprocal interactions between resveratrol and gut microbiota deepen our understanding of molecular mechanisms underlying its health benefits – LiangShen – Trends in Food Science & Technology

Synbiotics modulate gut microbiota and reduce enteritis and ventilator-associated pneumonia in patients with sepsis: a randomized controlled trial – Kentaro Shimizu – Critical Care

MICROBIAL ACTIVITY:

Relief from nitrogen starvation entails quick unexpected down-regulation of glycolytic/lipid metabolism genes in enological Saccharomyces cerevisiae– Catherine Tesnière – bioRxiv

ANTIMICROBIAL RESISTANCE:

Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River – Aneisha M. Collins – Applied and Environmental Science

SOIL MICROBIOME:

Book Chapter – Paddy Soil Microbial Diversity and Enzymatic Activity in Relation to Pollution – Muhammad Afzaal – Environmental Pollution of Paddy Soils

Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.) – Massimiliano Cardinale – Microbial Ecology

URINARY MICROBIOME:

Review – The Role of Urinary Microbiota in Lower Urinary Tract Dysfunction: A Systematic Review – TiagoAntunes-Lopes – European Urology Focus

ANIMAL MICROBIOME:

Ecological patterns in the skin microbiota of frogs from tropical Australia – Keith Christian – Ecology and Evolution

Oral Microbiota of the Snake Bothrops lanceolatus in Martinique – Dabor Résière – Int J Environ Res Public Health

MYCOBIOME:

Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates – Caleb Walker – Genome Sequences

GENERAL MICROBIOME:

Book Chapter – The Role and Future Possibilities of Next-Generation Sequencing in Studying Microbial Diversity – VijayNema – Microbial Diversity in the Genomic Era

GUT MICROBIOME:

Review – Association of obesity, diabetes and linked complications with gut microbiota – Amina Arif – Pure and Applied Biology

Bifidobacterial Dominance of the Gut in Early Life and Acquisition of Antimicrobial Resistance – Diana H. Taft – Clinical Science and Epidemiology

The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease – Tao Zuo – Frontiers in Microbiology

Influence of maternal factors on the rumen microbiome and subsequent host performance – Hannah C. Cunningham – Translational Animal Science

Colorectal carcinogenesis: an archetype of gut microbiota–host interaction – James L Alexander – Ecancermedicalscience

ANIMAL MODELS MICROBIOME:

Maternal Immune Activation Alters Adult Behavior, Gut Microbiome and Juvenile Brain Oscillations in Ferrets – Yuhui Li – eNeuro

PROBIOTICS:
Bacteriocin production of the probiotic Lactobacillus acidophilus KS400 – C. Gaspar – AMB Express

August 25 2018

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Todays Microbiome Digest covers the topics on microbiome of animalia kingdom ranging from humans ⇒mammals ⇒ amphibians ⇒ insects , cyanobacteria, AMR versus AMS, host microbe interactions, how & which microbes create homeostatis in the human body sites.  Happy Reading!

GUT or INTESTINAL MICROBIOME:

Gut microbiome: Microflora association with obesity and obesity-related comorbidities – Lone JB – Microb Pathog

Relevance of gut microbiota in cognition, behaviour and Alzheimer’s disease – de J R De-Paula V – Pharmacol Res.

Small intestinal microbiota: the neglected stepchild needed for fat digestion and absorption – Chang EB – Gut Microbes.

Prospects for Primary Prevention of Type 1 Diabetes by Restoring a Disappearing Microbe – Insel R – Pediatr Diabetes

ANIMAL MICROBIOME:

Synergetic action between the rumen microbiota and bovine health – Zeineldin M – Microb Pathog

Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig and mouse gut microbiomes – Li X – Gigascience

Analyses of Aerosol Concentrations and Bacterial Community Structures for Closed Cage Broiler Houses at Different Broiler Growth Stages in Winter – Jiang L – J Food
Prot.

Characterization of the bacterial community of braised chicken, a specialty poultry product in China – Liu DY – Poult Sci.

Metagenomics analysis reveals significant modulation of cecal microbiota of broilers fed palm kernel expeller diets – Chen WL- Poult Sci.

Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone – Xue D – J Microbiol.

INSECT MICROBIOME:

Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation –
Oliveira JL – PLoS Negl Trop Dis.

FISH MICROBIOME:

Dietary salt levels affect digestibility, intestinal gene expression, and the microbiome, in Nile tilapia (Oreochromis niloticus) – Hallali E – PLoS One

WATER MICROBIAL ECOLOGY:

Bacterial bioclusters relate to hydrochemistry in New Zealand groundwater – Sirisena KA – FEMS Microbiol Ecol

 

PLANT MICROBIOME:

Technique : Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures – Cornet L – Microb Genom

High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil – Bourceret
A – Environ Sci Pollut Res Int.

 

INFANT MICROBIOME:

Investigating the effects of cesarean delivery and antibiotic use in early childhood on risk of later attention deficit hyperactivity disorder – Axelsson PB – J Child
Psychol Psychiatry

 

PROBIOTICS or PREBIOTICS:

The effect of a multispecies probiotic on microbiota composition in a clinical trial of patients with diarrhea-predominant irritable bowel syndrome – Hod K –
Neurogastroenterol Motil.

ANTI- MICROBIAL RESISTANCE and SUSCEPTANCE:

Un-segregated waste disposal: an alarming threat of antimicrobials in surface and ground water sources in Delhi – Velpandian T – Environ Sci Pollut Res Int.

Novel bioactive peptides from PD-L1/2, a type 1 ribosome inactivating protein from Phytolacca dioica L. Evaluation of their antimicrobial properties and anti-biofilm
activities – Pizzo E – Biochim Biophys Acta

 

RESPIRATORY MICROBIOME:

Lower airway microbiota for ‘biomarker’ measurements of cystic fibrosis disease progression – Sherrard LJ – Thorax

Sputum microbiota is predictive of long-term clinical outcomes in young adults with cystic fibrosis – Acosta N- Thorax

 

HOST MICROBE INTERACTIONS:

Preventive effects of bovine colostrum supplementation in TNBS-induced colitis in mice – Filipescu IE – PLoS One

Role of wnt5a in metabolic inflammation in humans – Relling I – J Clin Endocrinol Metab.

 

TECHNIQUES:

Review: Evidence-Based Strategies for the Prehabilitation of the Abdominal Wall Reconstruction Patient – Joslyn NA – Plast Reconstr Surg.

QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling – Zheng B – Sci China Life Sci.

Review: Advances in Imaging Specific Mediators of Inflammatory Bowel Disease – Dmochowska N – Int J Mol Sci.

 

NUTRITION or DIET and TREATMENT:

Glucomannan hydrolysate promotes gut proliferative homeostasis and extends lifespan in Drosophila melanogaster – Si Y – J Gerontol A Biol Sci Med Sci.

Cultivable butyrate-producing bacteria of elderly Japanese diagnosed with Alzheimer’s disease – Nguyen TTT – J Microbiol.

Efficacy of Proanthocyanidins from Pelargonium sidoides Root Extract in Reducing P. gingivalis Viability While Preserving Oral Commensal S. salivarius – Savickiene N –
Materials (Basel).

Effects of Tempeh Fermentation with Lactobacillus plantarum and Rhizopus oligosporus on Streptozotocin-Induced Type II Diabetes Mellitus in Rats – Huang YC – Nutrients

July 8, 2018

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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

June 26, 2018

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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