Here’s your Digest before the US Thanksgiving holiday with a burst of human gut microbiome/animal experiment papers. Science publishes a special edition on diet and health, how do human gut microbes fare against mouse gut commensals, and watch out for the water used in your microbiome studies!
Jobs
Open Rank Tenure Track Faculty Position – Baylor College of Medicine
General microbiology
Preprint: Natural strain diversity reveals novel biofilm regulation in squid-colonizing Vibrio fischeri – Ella R. Rotman et al. – bioRxiv
Preprint: Genotyping of Salmonella spp. on the basis of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) – Calvin Jiksing et al. – bioRxiv
Pregnancy and early life
Iron-containing micronutrient powders modify the effect of oral antibiotics on the infant gut microbiome and increase post-antibiotic diarrhoea risk: a controlled study in Kenya – Daniela Paganini et al. – Gut
Human skin microbiome
Review: The epithelial immune microenvironment (EIME) in atopic dermatitis and psoriasis – Teruki Dainichi et al. – Nature Immunology
Human oral microbiome
The Effect of Influenza Virus on the Human Oropharyngeal Microbiome – Elisa Ramos-Sevillano et al. – Clinical Infectious Diseases
Human vaginal microbiome
Review: Ecological dynamics of the vaginal microbiome in relation to health and disease – Shirley Greenbaum et al. – American Journal of Obstetrics and Gynecology
Human gut microbiome
Preprint: Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome – Benjamin D. Ross et al. – bioRxiv
Review: Calorie restriction and its impact on gut microbial composition and global metabolism – Xiaojiao Zheng et al. – Frontiers of Medicine
Fecal microbiota transplantation with frozen capsules for a patient with refractory acute gut graft-versus-host disease – Satoshi Kaito et al. – Blood Advances
Review: Salts and energy balance: A special role for dietary salts in metabolic syndrome –
Christopher W.Brey et al. – Clinical Nutrition
IL23R-protective coding variant promotes beneficial bacteria and diversity in the ileal microbiome in healthy individuals without inflammatory bowel disease – Martha Zakrzewski et al. – Journal of Crohn’s and Colitis
In vitro: A four-strain probiotic exerts positive immunomodulatory effects by enhancing colonic butyrate production in vitro – Frédéric Moens et al. – International Journal of Pharmaceutics
Review: Obesity and Cancer Risk: Emerging biological mechanisms and perspectives – Konstantinos I. Avgerinos et al. – Metabolism
Review: Endocrine regulation of gut function – a role for glucagon-like peptide-1 in the pathophysiology of irritable bowel syndrome – Dervla O’Malley – Experimental Physiology
The Human Metabolism of Nuts Proanthocyanidins Does not Reveal Urinary Metabolites Consistent with Distinctive Gut Microbiota Metabotypes – Adrián Cortés‐Martín et al. – Molecular Nutrition & Food Research
Review: The role of dietary factors in inflammatory bowel diseases: new perspectives – Yi Quan Zhou et al. – Journal of Digestive Diseases
Review: Interaction of gut microbiota with dysregulation of bile acids in the pathogenesis of nonalcoholic fatty liver disease and potential therapeutic implications of probiotics – Jiezhong Chen et al. – Journal of Cellular Biochemistry
Review: Cross-Talk Between Gluten, Intestinal Microbiota and Intestinal Mucosa in Celiac Disease: Recent Advances and Basis of Autoimmunity – Atul Munish Chander et al. – Frontiers in Microbiology
Review: Control and dysregulation of redox signalling in the gastrointestinal tract – Eric L. Campbell & Sean P. Colgan – Nature Reviews Gastroenterology & Hepatology
** Review: The gut microbiota at the intersection of diet and human health – Christopher L. Gentile & Tiffany L. Weir – Science
Review: Gut Microbiota and Their Neuroinflammatory Implications in Alzheimer’s Disease – Vo Van Giau et al. – Nutrients
Review: Gut microbiota in diabetes and HIV: Inflammation is the link – Vicente Estrada & Noemi Gonzalez – EBioMedicine
Human gut-microbiome-brain axis
Can the gut be the missing piece in uncovering PD pathogenesis? – Guillaume Chapelet et al. – Parkinsonism & Related Disorders
Human multi-site microbiome
Characterization of human breast tissue microbiota from core needle biopsies through the analysis of multi hypervariable 16S-rRNA gene regions – Lara Costantini et al. – Scientific Reports
Review: Estimating the postmortem interval using microbes: Knowledge gaps and a path to technology adoption – Jessica L.Metcalf – Forensic Science International: Genetics
Boston Type I Keratoprosthesis: Antibacterial Resistance and Microbiota Evaluation of Soft Contact Lenses – Emilio A.Torres-Netto et al. – American Journal of Ophthalmology
Food microbiome
Combined effects of thymol, carvacrol and packaging on the shelf-life of marinated chicken – Layal Karam et al. – International Journal of Food Microbiology
Effect of post-harvest interventions on surficial carrot bacterial community dynamics, pathogen survival, and antibiotic resistance – Vaishali Dharmarha et al. – International Journal of Food Microbiology
The potential use of probiotic and beneficial bacteria in the Brazilian dairy industry – Monique Colombo et al. – Journal of Dairy Research
Animal experiments
In vitro: Environmental pollutant-mediated disruption of gut microbial metabolism of the prebiotic inulin – Jessie Hoffman et al. – Anaerobe
Assessment of the adverse impacts of aflatoxin B1 on gut-microbiota dependent metabolism in F344 rats – Jun Zhou et al. – Chemosphere
Dietary Tomato Powder Inhibits High-Fat Diet-Promoted Hepatocellular Carcinoma with Alteration of Gut Microbiota in Mice Lacking Carotenoid Cleavage Enzymes – Hui Xia et al. – Cancer Prevention Research
Chronic intermittent hypoxia disrupts cardiorespiratory homeostasis and gut microbiota composition in adult male guinea-pigs – Eric F.Lucking et al. – EBioMedicine
Microbiota-Derived Lactate Activates Production of Reactive Oxygen Species by the Intestinal NADPH Oxidase Nox and Shortens Drosophila Lifespan – Igor Iatsenko et al. – Immunity
A polysaccharide extracted from Astragalus membranaceus residue improves cognitive dysfunction by altering gut microbiota in diabetic mice – Yameng Liu et al. – Carbohydrate Polymers
Mouse: Role of Bile Acids and GLP-1 in Mediating the Metabolic Improvements of Bariatric Surgery – Vance L. Albaugh et al. – Gastroenterology
Evaluation of Sialyllactose Supplementation of a Prebiotic-Containing Formula on Growth, Intestinal Development, and Bacterial Colonization in the Neonatal Piglet – Marcia H Monaco et al. – Current Developments in Nutrition
Mouse: The Probiotic Effectiveness in Preventing Experimental Colitis Is Correlated With Host Gut Microbiota – Sharmila Suwal et al. – Frontiers in Microbiology
Soy-Induced Fecal Metabolome Changes in Ovariectomized and Intact Female Rats: Relationship with Cardiometabolic Health – Victoria J. Vieira-Potter et al. – Scientific Reports
** Selective colonization ability of human fecal microbes in different mouse gut environments – Wei Zhou et al. – The ISME Journal
Rat: Potential Involvement of Peripheral Leptin/STAT3 Signaling in the Effects of Resveratrol and Its Metabolites on Reducing Body Fat Accumulation – Andrea Ardid-Ruiz et al. – Nutrients
Bacteria engineered to produce IL-22 in intestine induce expression of REG3G to reduce ethanol-induced liver disease in mice – Tim Hendrikx et al. – Gut
Effects of polystyrene microplastics on the composition of the microbiome and metabolism in larval zebrafish – Zhiqin Wan et al. – Chemosphere
Animal microbiome
The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production – A.K. Vasquez et al. – Journal of Dairy Science
Plant, root and soil microbiome
Community diversity and potential functions of rhizosphere-associated bacteria of nickel hyperaccumulators found in Albania – Séverine Lopez et al. – Science of The Total Environment
Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum – Ye Sun et al. – International Journal of Systematic and Evolutionary Microbiology
Linking bacterial community composition to soil salinity along environmental gradients – Kristin M. Rath et al. – The ISME Journal
Soil microbial community composition closely associates with specific enzyme activities and soil carbon chemistry in a long-term nitrogen fertilized grassland – Yue Li et al. – Science of The Total Environment
Water and extremophile microbiome
Periodic and spatial spreading of alkanes and Alcanivorax bacteria in deep waters of the Mariana Trench – Wen-Li Li et al. – Applied and Environmental Microbiology
Distinct bacterial and archaeal diversities and spatial distributions in surface sediments of the Arctic Ocean – Yuguang Wang et al. – FEMS Microbiology Letters
Microbial subnetworks related to short-term diel O2 fluxes within geochemically distinct freshwater wetlands – Dean J Horton et al. – FEMS Microbiology Letters
Adaptive shifts of bacterioplankton communities in response to nitrogen enrichment in a highly polluted river – Yuzhan Yang et al. – FEMS Microbiology Letters
Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments – Luis J. Perez Calderon et al. – MicrobiologyOpen
Phages and viruses
Preprint: Complete genome of a Measles virus from Roraima state, Brazil – Catia Meneses et al. – bioRxiv
Safety Studies of Pneumococcal Endolysins Cpl-1 and Pal – Marek Harhala et al. – Viruses
Technology
Preprint: Controlling complex microbial communities: a network-based approach – Marco Tulio Angulo et al. – bioRxiv
** H2Oh No! The importance of reporting your water source in your in vivo microbiome studies – Jacqueline A. Barnett & Deanna L. Gibson – Gut Microbes
Bioinformatics
Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut – Yoshihisa Wakita et al. – BMC Microbiology
Non-microbiology picks
Preprint: Benchmarking university medical centres for responsible metrics. A cross sectional study on timely results dissemination across 36 German centres – Susanne Wieschowski et al. – bioRxiv
Microbiome Digest - Bik's Picks 