December 16, 2018

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.

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