May 4, 2021

In today’s post – host-microbe marker for inflammatory bowel disease, evolution of soil bacterium along the climate gradient, how C. difficile exploits host metabolite under inflammatory conditions induced by its own toxins and differential response of commensals to alter C. difficle virulence.

Job Posting

Microbiome Scientific Researcher, Computational (Cancer Immunology) – Genentech South San Francisco, California

General Microbiome

Endothelium–gut communication: IGF‐1Rs crosstalk with microbiota – Zhen Bouman Chen – EMBO reports

Recent advances in marine algae oligosaccharides: structure, analysis, and potential prebiotic activities – Xu-Ting Xie – Critical Reviews in Food Science and Nutrition

Human Microbiome

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men – Jun Li – Gut

Gut Dysbiosis Associated with Antibiotics and Disease Severity and Its Relation to Mortality in Critically Ill Patients – Masahiro Ojima – Digestive Diseases and Sciences

Effects of Totum-63 on glucose homeostasis and post-prandial glycemia: a translational study – Vivien Chavanelle – American Journal of Physiology Endocrinology and Metabolism

Impact of a fermented soy beverage supplemented with acerola by-product on the gut microbiota from lean and obese subjects using an in vitro model of the human colon – Antonio Diogo Silva Vieira – Environmental biotechnology

Decoding the matrix: multiomics reveals host-microbe biomarker for inflammatory bowel disease – Monica Viladomiu – The Journal of Clinical Investigation

Animal Microbiome

C. difficile exploits a host metabolite produced during toxin-mediated disease – Kali M. Pruss – Nature

In vivo commensal control of Clostridioides difficile virulence – Brintha P. Girinathan – BioRxiv

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing – Neoklis Apostolopoulos – PlosOne

Plant, root and soil microbiome

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient – Alexander B. Chase – PNAS

Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation – Spencer Diamond – BioRxiv

Water microbiome

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem – Ya-Jou Chen – ISME Journal

Techniques

Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S – Yi‐Chun Yeh – Environmental Microbiology

Bacteria

Completion of the gut microbial epi-bile acid pathway – Heidi L. Doden – Gut Microbes

Possible effects of Porphyromonas gingivalis on the blood-brain barrier in Alzheimer’s disease – Ingar Olsen – Expert Review of Anti-infective Therapy

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii – Tao Luo – Nature Communications

February 24, 2021

Today’s digest is about functional analyses of microbial community in anoxic sites, microbial life in billions of years old fluid inclusions, development and use of human skin commensal, expanded pig metagenome catalogue and a brilliant review on advances in RNAseq technologies to decipher host-microbiota interactions. Happy reading!

General microbiome

Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites – Alexandra Kristin Bashir – Microbiome

Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov., isolated from raw milk in Germany – Stefanie Gieschler – International Journal of Systematic and Evolutionary Microbiology

Human microbiome

Development of a human skin commensal microbe for bacteriotherapy of atopic dermatitis and use in a phase 1 randomized clinical trial – Teruaki Nakatsuji – Nature Medicine

Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation – Travis T. Sims – Communications Biology

Characterization of the human skin resistome and identification of two microbiota cutotypes – Zhiming Li – Microbiome

Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions – Hee Sang You – FEMS Microbiology Letters

Animal microbiome

Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress – Weijie Zhang – Translational Psychiatry

Ginsenoside Rk3 Ameliorates Obesity-Induced Colitis by Regulating of Intestinal Flora and the TLR4/NF-κB Signaling Pathway in C57BL/6 Mice – Hongwei Chen – Journal of Agricultural and Food Chemistry

Dietary anthocyanin-rich extract of açai protects from diet-induced obesity, liver steatosis, and insulin resistance with modulation of gut microbiota in mice – Haizhao Song – Nutrition

Effects of supplementing sow diets during late gestation with Pennisetum purpureum on antioxidant indices, immune parameters and faecal microbiota – Peng‐Fei Huang – veterinary Medicine and Science

Alterations in the gut microbiome and metabolic profile in rats acclimated to high environmental temperature – Yang Cao – Microbial Biotechnology

The pelvic flexure separates distinct microbial communities in the equine hindgut – Kailee J. Reed – Scientific Reports

Effects of urolithins on obesity-associated gut dysbiosis in rats fed on a high-fat diet – Abdulrasheed O. Abdulrahman – International Journal of Food Sciences and Nutrition

Functional Foods

Prebiotic Lactulose Ameliorates the Cognitive Deficit in Alzheimer’s Disease Mouse Model through Macroautophagy and Chaperone-Mediated Autophagy Pathways – Yan-Suan Lee – Journal of Agricultural and Food Chemistry

Water microbiome

Ingredients for microbial life preserved in 3.5 billion-year-old fluid inclusions – Helge Mißbach – Nature Communications

Techniques

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome – Congying Chen – Nature Communications

Cross-species RNA-seq for deciphering host–microbe interactions – Alexander J. Westermann – Nature Reviews Genetics

Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection – Michael A. Henson – Plos Computational Biology

An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants – Sivapriya Ramamoorthy – BMC Microbiology

Ecological rules for the assembly of microbiome communities – Katharine Z. Coyte – Plos Biology

February 9, 2021

Today’s updates in microbiome – iron homeostasis in host and gut bacteria, flavonol catabolism in gut bacteria, protocol for characterization of pulmonary microbiota, how single bacterial strain prevents GVHD and many more… happy reading!

General microbiome

Iron homeostasis in host and gut bacteria – a complex interrelationship – Yohannes Seyoum – Gut Microbes

α1-3Gal antigen in gut microbiota, a potential new environmental factor in multiple sclerosis – LéoBoussamet – Clinical Immunology

Human microbiome

Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy – Taraprasad Das – Scientific Reports

Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria – Gaohua Yang – Nature Communications

Animal microbiome

A single strain of Bacteroides fragilis protects gut integrity and reduces GVHD – M. Hanief Sofi – JCI Insight

Social behavior of musk deer during the mating season potentially influences the diversity of their gut microbiome – Jianmei Li​ – PeerJ

Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota – Jianzhong Hu – Scientific Reports

Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community – Jessica A. Lee – Microorganisms

Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome – LeeMin-Ting – Journal of Lipid Research

Functional Foods

Shaping the Future of Probiotics and Prebiotics – Marla Cunningham – Trends in Microbiology

Utilizing the Food–Pathogen Metabolome to Putatively Identify Biomarkers for the Detection of Shiga Toxin-Producing E. coli (STEC) from Spinach – Snehal R. Jadhav – Metabolites

Clinical effects and gut microbiota changes of using probiotics, prebiotics or synbiotics in inflammatory bowel disease: a systematic review and meta-analysis – Xiao-Feng Zhang – European Journal of Nutrition

Diabetes-induced cardiomyopathy is ameliorated by heat-killed Lactobacillus reuteri GMNL-263 in diabetic rats via the repression of the toll-like receptor 4 pathway – Chung-Jen Chiang – European Journal of Nutrition

Water microbiome

Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater – Blanca M. Gonzalez-Silva – Scientific Reports

The microbial dimension of submarine groundwater discharge:current challenges and future directions – Clara Ruiz-González- FEMS Microbiology Reviews

Estrogen induces shift in abundances of specific groups of the coral microbiome – Caren L. S. Vilela – Scientific Reports

Metabolic fingerprinting of the Antarctic cyanolichen Leptogium puberulum–associated bacterial community (Western Shore of Admiralty Bay, King George Island, Maritime Antarctica) – Jakub Grzesiak – Microbial Ecology

Techniques

Development of a robust protocol for the characterization of the pulmonary microbiota – Nathan Dumont-Leblond – Nature Communications

Microbes in news

Eating fat-rich foods as a child causes long-lasting changes in gut microbiome: Study – First post

Human Microbiome Market Set to Register Healthy CAGR During to 2026 – KSU The Sentinel Newspaper

January 26, 2021

Review articles on hygiene hypothesis and COVID, role of microbiome in cancer, different studies on efficacy of probiotics in inflammatory and metabolic diseases, and many more…

General microbiome

The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome – B. Brett Finlay – PNAS

Exploring the Role of Gut Microbiome in Colon Cancer – Indranil Chattopadhyay – Applied Biochemistry and Biotechnology

Cancer trigger or remedy: two faces of the human microbiome – Anna Grenda – Applied Microbiology and Biotechnology

Human microbiome

Microbiota, Epigenetics and Trained Immunity: Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood – Susan V Lynch – American Journal of Respiratory and Critical Care Medicine

Gut Microbial Signature of Hepatocellular Cancer in Men with Cirrhosis – Somaya Albhaisi – Liver Transplantation

An Evaluation of the Fecal Microbiome in Lynch Syndrome – Adalberto Gonzalez – Journal of Gastrointestinal Cancer

Gut microbiota condition the therapeutic efficacy of trastuzumab in HER2-positive breast cancer – Martina Di Modica – Cancer Research

Recent, mid-, and late-adulthood antibiotic use are associated with subsequent risk of diverticulitis – Long H.Nguyen – Gastroenterology

Animal microbiome

Gestational gut microbial remodeling is impaired in a rat model of preeclampsia superimposed on chronic hypertension – Jeanne A Ishimwe – Physiological Genomics

Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas – Leijin – Science of the Total Environment

Functional Foods

Probiotic Lactobacillus casei Shirota prevents acute liver injury by reshaping the gut microbiota to alleviate excessive inflammation and metabolic disorders – Ren Yan – Microbial Biotechnology

Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses – Miriam Zago – PlosOne

The Acid-Dependent and Independent Effects of Lactobacillus acidophilus CL1285, Lacticaseibacillus casei LBC80R, and Lacticaseibacillus rhamnosus CLR2 on Clostridioides difficile R20291 – Sathursha Gunaratnam – Probiotics and Antimicrobial Proteins

Polyphosphate, Derived from Lactobacillus brevis, Modulates the Intestinal Microbiome and Attenuates Acute Pancreatitis – Shuhei Takauji – Digestive Diseases and Sciences

Human Intestinal Barrier: Effects of Stressors, Diet, Prebiotics, and Probiotics – Michael Camilleri – Clinical and Translational Gastroenterology

Plant, root and soil microbiome

Insights into the plant responses to drought and decoding the potential of root associated microbiome for inducing drought tolerance – Piyush Mathur – Physiologia Plantarum

Water microbiome

A genomic view of the microbiome of coral reef demosponges – S. J. Robbins – ISME Journal

Microbes in news

Gut Bacteria Offer Insight into Molecules Protective Against Asthma and COVID-19 – Biospace

January 21, 2021

Today’s post include review article on gut-liver axis, research articles on diet-microbiota interaction in Chinese adults, association between microbiome and type1 diabetes, and new metagenomic profiling method using phylogenetic markers.

General microbiome

Bacterial and eukaryotic extracellular vesicles and non-alcoholic fatty liver disease: new players in the gut-liver axis? – Alexandre Villard – American Joural of Physiology Gastrointestinal and Liver Physiology

Potential Contribution of the Intestinal Microbiome to Phenethylamine-Induced Hyperthermia – Aburahma A. – Brain, Behavior and Evolution

Human microbiome

Long-term diet quality is associated with gut microbiome diversity and composition among urban Chinese adults – Danxia Yu – American Journal of Clinical Nutrition

Long-term dietary intake from infancy to late adolescence is associated with gut microbiota composition in young adulthood – Kolade Oluwagbemigun – American Journal of Clinical Nutrition

The gut microbiota metabolite propionate ameliorates intestinal epithelial barrier dysfunction-mediated Parkinson’s disease via the AKT signaling pathway – Tingting Huang – Neuroreport

Fecal and mucosal microbiota profiling in pediatric inflammatory bowel diseases – Lorenza Putignani – European Journal of Gastroenterology and Hepatology

Associations between diet, the gut microbiome and short chain fatty acids in youth with islet autoimmunity and type 1 diabetes – Jessica E. Harbison – Pediatric Diabetes

Reproducing the scalp microbiota community: co‐colonization of a 3D reconstructed human epidermis with C. acnes and M. restricta – Marisa Melon – International Journal of Cosmetic Science

Hepatic steatosis relates to gastrointestinal microbiota changes in obese girls with polycystic ovary syndrome – Beza Jobira – PlosOne

Animal microbiome

Infection trains the host for microbiota-enhanced resistance to pathogens – Apollo Stacy – Cell

Changes of Gut Microbiota and Its Correlation With Short Chain Fatty Acids and Bioamine in Piglets at the Early Growth Stage – Renli Qi – Frontiers in Veterinary Science

Functional Foods

Prospecting Human Milk Oligosaccharides as a Defense Against Viral Infections – Rebecca E Moore- ACS Infectious Diseases

Techniques

TIPP2: metagenomic taxonomic profiling using phylogenetic markers – Nidhi Shah – Bioinformatics

Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water – Meghan Maguire – PlosOne

Microbes in news

Your Microbiome Isn’t Shaped Just By What You Feed It – Discover

Taurine Enhances the Microbiome’s Resistance to Future Pathogens – Genetic Engineering and Biotech News

October 13, 2020

Today’s mid-week digest is about – meta analysis of metabolic benefits of probiotics, probiotics and synbiotics, microbiome association with narcolepsy type 1, design of microbial consortium for reduced C. difficle colonization, new sequencing technique for pathogen identification in cerebrospinal fluid and many more… Happy reading!

Human microbiome

The effect of probiotics, prebiotics or synbiotics on metabolic outcomes in individuals with diabetes: a systematic review and meta-analysis – Patricia M. Bock – Diabetologia

Effect of a Nonoptimal Cervicovaginal Microbiota and Psychosocial Stress on Recurrent Spontaneous Preterm Birth – Kristin D. Gerson – American Journal of Perinatology

Targeting the microbiome-gut-brain axis for improving cognition in schizophrenia and major mood disorders: A narrative review – Miquel Bioque – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Inflammatory Bowel Disease Environmental Risk Factors: Diet and Gut Microbiota – Sarah Altajar – Current Gastroenterology Reports

Co‐ and polymicrobial infections in the gut mucosa: the host‐microbiota‐pathogen perspective – Teresa Frisan – Cellular Microbiology

Gut microbiota composition is associated with narcolepsy type 1 – Alexandre Lecomte – Neurology

A parental transcriptional response to microsporidia infection induces inherited immunity in offspring – Alexandra R. Willis – BioRxiv

Melamine contamination and associated health risks: Gut microbiota does make a difference – Meenakshi Rajpoot – Biotechnology and Applied Biochemistry

Animal microbiome

Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization – Fátima C. Pereira – Nature Communications

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs – I. I. de Winter – Scientific Reports

Bacterial community analysis on the different mucosal immune inductive sites of gastrointestinal tract in Bactrian camels – Wang-Dong Zhang – PlosOne

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status – Guillaume Larivière‐Gauthier – Letters in Applied Microbiology

Plant, root and soil microbiome

Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow – Ruifen Zhu – Scientific Reports

Evidence for signatures of ancient microbial life in paleosols – Katharina Frindte – Scientific Reports

Techniques

Pathogen identification in culture-negative cerebrospinal fluid specimens of patients with purulent meningitis using next-generation sequencing technology – Xin Men – International Journal of Clinical Experimental Pathology

October 2, 2020

Today’s exciting updates – FMT method to restore normal microbial development in caesarean-born infants, mechanism unveiled how dietary tryptophan improves alcohol induced liver injury, advance in droplet based microfluidics to study host-microbiome interactions, prebiotics encapsulation of probiotic to suppress colon cancer and new hope to curb plastic waste by discovery of plastic-eating enzyme cocktail. Happy weekend, stay safe!

General microbiome

Eligible blood donors’ decisions about donating stool for fecal microbiota transplantation: Does ambivalence play a role? – Melissa K. Hyde – Transfusion

Microbiota-Dependent Effects of IL-22 – Morsal Sabihi – Cells

Human microbiome

Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study – Katri Korpela – Cell

Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases – Ji In Park – Scientific Reports

Dysbiosis in the oral microbiomes of anti-CCP positive individuals at risk of developing rheumatoid arthritis – Zijian Cheng – Annals of the Rheumatic Diseases

Animal microbiome

Microbiota tryptophan metabolism induces aryl hydrocarbon receptor activation and improves alcohol-induced liver injury – Laura Wrzosek – Gut

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients – Alfonsina D’Amato – Microbiome

Competitive reduction of poultry-borne enteric bacterial pathogens in chicken gut with bioactive Lactobacillus casei – Zajeba Tabashsum – Scientific Reports

Offspring susceptibility to metabolic alterations due to maternal high-fat diet and the impact of inhaled ozone used as a stressor – Samantha J. Snow – Scientific Reports

Beneficial effects of mung bean seed coat on the prevention of high-fat diet-induced obesity and the modulation of gut microbiota in mice – Dianzhi Hou – European Journal of Nutrition

Prebiotics‐Encapsulated Probiotic Spores Regulate Gut Microbiota and Suppress Colon Cancer – Di‐Wei Zheng – Advanced Materials

Multi-Omic Analysis Reveals Different Effects of Sulforaphane on the Microbiome and Metabolome in Old Compared to Young Mice – Se-Ran Jun – Microorganisms

Plant microbiome

Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes – Stefan Geisen – Isme Journal

Techniques

Investigating host-microbiome interactions by droplet based microfluidics – Alexandra S. Tauzin – Microbiome

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis – Sidney P. Walker – Scientific Reports

Non-microbiology picks

Plastic-eating enzyme ‘cocktail’ heralds new hope for plastic waste – Science Daily

September 1, 2020

Today’s post consists of review article on short chain fatty acids, research articles on efficacy of fecal microbiota transplant in patients with C. difficle infection and comorbities, identification of potential microbial biomarkers for preterm birth and a new technique to perform ultrafast microbial community analysis. Happy reading!

General microbiome

A systematic review of the effect of dietary pulses on microbial populations inhabiting the human gut – C.P.F. Marinangeli – Beneficial Microbes

Short chain fatty acids in human gut and metabolic health – E E Blaak – Beneficial Microbes

Human microbiome

The gut microbiome–derived metabolite trimethylamine N-oxide modulates neuroinflammation and cognitive function with aging – Vienna E. Brunt – Geroscience

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak – Microbiome

Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Patients With Multiple Comorbidities: Long-Term Safety and Efficacy Results From a Tertiary Care Community Hospital – Charumathi Raghu Subramanian – Gastroenterology Research

Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection – Matthew Magruder – Gut Microbes

Leveraging sequence‐based faecal microbial community survey data to identify alterations in gut microbiota among patients with Parkinson’s disease – Tianyi Ji – European Journal of Neuroscience

Plasma enterobacterial ClpB levels and ClpB- and α-MSH–reactive immunoglobulins in lung cancer patients with and without anorexia – Alessio Molfino – Nutrition

Identification of Potential Biomarkers in the Cervicovaginal Fluid by Metabolic Profiling for Preterm Birth – AbuZar Ansari – Metabolites

Plant microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied and Environmental Microbiology

Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth – Inga Tamošiūnė – Frontiers in Plant Science

Water microbiome

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu – Microbiome

Techniques

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Non-microbiology picks

Clinical characteristics of children and young people hospitalised with covid-19 in the United Kingdom: prospective multicentre observational cohort study – Olivia V Swann – BMJ

August 13, 2020

Today’s updates – microbiome connections in various disease cohorts such as gastric cancer, IBD, anorexia nervosa, obesity and diabetes; information on gut bacterial polyphosphates and o-glycanases and their role in host immunity and mucin breakdown; and new sequencing strategies to identify antibiotic-resistant genes. Happy reading!

General microbiome

Gut microbiota and COVID-19: A superfluous diagnostic biomarker or therapeutic target? – Emily Klann – Clinical Infectious Diseases

Engineered Live Biotherapeutics: Progress and Challenges – Yang Tan – Biotechnology Journal

Human microbiome

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity – Lianmin Chen – Nature Communications

Multi-omics data integration in anorexia nervosa patients before and after weight regain: A microbiome-metabolomics investigation – Alessio Maria Monteleone – Clinical Nutrition

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci – Bruno Cavadas – Microorganisms

Faecal microbiota signatures of IBD and their relation to diagnosis, disease phenotype, inflammation, treatment escalation and anti-TNF response in a European Multicentre Study (IBD-Character) – S. Vatn – Scandinavian Journal of Gastroenterology

A randomized crossover trial on the effect of plant-based compared with animal-based meat on trimethylamine-N-oxide and cardiovascular disease risk factors in generally healthy adults: Study With Appetizing Plantfood—Meat Eating Alternative Trial (SWAP-MEAT) – Anthony Crimarco – Americal Journal of Clinical Nutrition

Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response – Monta Ustinova – PlosOne

Microbial Profile During Pericoronitis and Microbiota Shift After Treatment – Xiuling Huang – Frontiers in Microbiology

Animal experiments

Unraveling the camel rumen microbiome through metaculturomics approach for agriculture waste hydrolytic potential – Shweta Srivastava – Archives of Microbiology

Bacterial polyphosphates interfere with the innate host defense to infection – Julian Roewe – Nature Communications

Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown – Lucy I. Crouch – Nature Communications

Nostoc sphaeroids Kütz polysaccharide and powder enrich a core bacterial community on C57BL/6j mice – Meixia Li – International Journal of Biological Macromolecules

Maternal dietary omega-3 deficiency worsens the deleterious effects of prenatal inflammation on the gut-brain axis in the offspring across lifetime – Q. Leyrolle – Neuropsychopharmacology

Water microbiome

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community – Pratibha Panwar – Microbiome

Techniques

Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses – Chiara Vanni – BioRxiv

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms – Rebecca Yee – European Journal of Clinical Microbiology & Infectious Diseases

July 23, 2020

In today’s digest – duodenal microbiota linked to stunting in children, differential effects of germfree and antibiotic treated mouse models on social behavior, microbial metabolite receptor GPBAR and its interaction with bile acids, review article on engineering microbes to treat diseases and many more…happy reading!

General microbiome

The Microbiota-Gut-Immune-Glia (MGIG) Axis in Major Depression – Leszek Rudzki – Molecular Neurobiology

Engineering the gut microbiota to treat chronic diseases – Noura S. Dosoky – Applied Microbiology and Biotechnology

Human microbiome

Acute and chronic improvement in postprandial glucose metabolism by a diet resembling the traditional Mediterranean dietary pattern: Can SCFAs play a role? – Marilena Vitale – Clinical Nutrition

Linking the duodenal microbiota to stunting in a cohort of undernourished Bangladeshi children with enteropathy – Robert Y. Chen – New England Journal of Medicine

Enterobacterales Infection after Intestinal Dominance in Hospitalized Patients – Krishna Rao – mSphere

Differences in the gut Firmicutes to Bacteroidetes ratio across age groups in healthy Ukrainian population – Alexander Vaiserman – BMC Microbiology

Preprint- Association of gut microbiota with cerebral cortex and cerebrovascular abnormality in human mild traumatic brain injury – Lijun Bai – BioRxiv

Real-world study in infants fed an infant formula with two human milk oligosaccharides – Enriqueta Román – Nutricion Hospitalaria

Animal experiments

Gut microbiome composition differences among breeds impact feed efficiency in swine – Matteo Bergamaschi – Microbiome

Opposing effects of antibiotics and germ-free status on neuropeptide systems involved in social behaviour and pain regulation – Katerina V. A. Johnson – BMC Neuroscience

Local Necrotic Cells Trigger Systemic Immune Activation via Gut Microbiome Dysbiosis in Drosophila – Hina Kosakamoto – Cell Reports

Peanut skin extract ameliorates the symptoms of type 2 diabetes mellitus in mice by alleviating inflammation and maintaining gut microbiota homeostasis – Lan Xiang – Aging

Preprint- Community composition and development of the post-weaning piglet gut microbiome – D. Gaio – BioRxiv

Gut microbiota regulate tumor metastasis via circRNA/miRNA networks – Zhuxian Zhua – Gut Microbes

Porcine circovirus type 2 (PCV2) and Campylobacter infection induce diarrhea in piglets: Microbial dysbiosis and intestinal disorder – Gang Yang – Animal Nutrition

Plant, root and soil microbiome

Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota – Sarah Huet – Frontiers in Plant Science

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat – Aymé Spor – Scientific Reports

Water microbiome

Preprint- Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs – A. Meziti – BioRxiv

Preprint- Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing – Kimothy L. Smith – BioRxiv

Phages and Viruses

Preprint- Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract – Sabrina I. Green – BioRxiv

Techniques
Structural basis of GPBAR activation and bile acid recognition – Fan Yang – Nature

Microbes in News

Machine learning analysis reveals less diverse microbiome in children with type 1 diabetes – Healio