Today’s digest includes some new bioinformatics techniques to study the microbiome and some more cool papers about diet and the microbiome.

General Microbiome

Experimental evolution reveals microbial traits for association with the host gut. – Vega NM – PLoS Biology

Human gut Microbiome

The intestinal microbiota predisposes to traveler’s diarrhea and to the carriage of multidrug-resistant Enterobacteriaceae after traveling to tropical regions. – Leo S – Gut Microbes

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome – Jun Li – bioRxiv

Human Pregnancy/Infant Microbiome

Effect of Delivery Mode and Nutrition on Gut Microbiota in Neonates. – Akagawa S – Annals of Nutrition and Metabolism

Trait-based community assembly and succession of the infant gut microbiome – John Guittar – Nature Communications

Animal experiments

Modulation of Gut Microbiota Composition by Serotonin Signaling Influences Intestinal Immune Response and Susceptibility to Colitis. – Kwon YH – Cellular and Molecular Gastroenterology and Hepatology

Plant, root, water and soil Microbiome

Marine biofilms constitute a bank of hidden microbial diversity and functional potential – Weipeng Zhang – Nature Communications

Combined metabarcoding and co-occurrence network analysis to profile the bacterial, fungal and Fusarium communities and their interactions in maize stalks – Jose F. Cobo-Diaz – Frontiers in Microbiology

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Bioinformatics

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion – Sabine Koch – PLoS Computational Biology

Swathi’s non-microbiology picks

How Millennials Became The Burnout Generation – An article about work-life balance that I think is applicable to scientists and academia.

Happy New Year Everyone! Some cool new papers for the digest including multiple diet studies!

General Microbiome

Cultivated human vaginal microbiome communities impact Zika and Herpes Simplex Virus replication in ex vivo vaginal mucosal cultures – Megan H Amerson-Brown – Frontiers in Microbiology

Human gut Microbiome

In vivo screening of multiple bacterial strains identifies Lactobacillus rhamnosus Lb102 and Bifidobacterium animalis ssp. lactis Bf141 as probiotics that improve metabolic disorders in a mouse model of obesity – Le Barz M – FASEB Journal

Protective effects of Bacillus probiotics against high-fat diet-induced metabolic disorders in mice. – Kim B – PLoS One

NLRP1 restricts butyrate producing commensals to exacerbate inflammatory bowel disease. – Tye H – Nature Communications

Human Pregnancy Microbiome

Characterizing the Subgingival Microbiome of Pregnant African American Women. – Yang I – J Obstet Gynecol Neonatal Nurs

Animal experiments 

A Gut Commensal Bacterium Promotes Mosquito Permissiveness to Arboviruses. – Wu P – Cell Host Microbe

Plant, root, and soil Microbiome

Specific recruitment of soil bacteria and fungi decomposers following a biostimulant application increased crop residues mineralization. – Hellequin E – PLoS One

Mangrove facies drives resistance and resilience of sediment microbes exposed to anthropic disturbance – C Capdeville – Frontiers in Microbiology

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Bioinformatics

Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur – Hiltemann SD – Gigascience

iVikodak–a platform and standard workflow for inferring, analyzing, comparing, and visualizing the functional potential of microbial communities – S Nagpal -Frontiers in Microbiology

Swathi’s non-microbiology picks

Issac Asimov on his predictions for 2019 – Issac Asimov

Good morning everyone, Today’s digest mainly focusing on the methods such as SigClust a novel clustering algorithm, mm-tSNE a method for visualizing high-dimensional data and aMiAD – a novel microbial diversity association test. Additionally, several review articles and research using human as well as animal experiments showing the relationship of the gut microbiome in Alzheimer’s, Parkinson, atopic dermatitis, antidepressant and anti-inflammatory, heart failure, NAFLD, irritable bowel syndrome and colorectal cancer and their role in the protection against the acute arsenic toxicity. Enjoy Reading.

General microbiome

Review: The microbiome of the nose – Matthew Rawls – Annals of Allergy, Asthma, and Immunology

The Gut Microbiome in Food Allergy – William Zhao – Annals of Allergy, Asthma, and Immunology

Prenatal stress enhances postnatal plasticity: The role of microbiota – Sarah Hartman – Developmental Psychobiology

Review: The gut microbiome and heart failure – Adilah F. Ahmad – Current Opinion in Cardiology

Synthetic consortia of nanobody‐coupled and formatted bacteria for prophylaxis and therapy interventions targeting microbiome dysbiosis‐associated diseases and co‐morbidities – Kenneth Timmis – Microbial Biotechnology

Gut microbiome

The gut microbiota-derived metabolite trimethylamine N-oxide is elevated in Alzheimer’s disease – Nicholas M. Vogt – Alzheimer’s Research & Therapy

Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study – Martin Steen Mortensen – BMC Microbiology

Effects of diet on the childhood gut microbiome and its implications for atopic dermatitis – Mahboobeh Mahdavinia – The Journal of Allergy and Clinical Immunology

Editorial: Emerging evidence linking the gut microbiome to neurologic disorders – Jessica A. Griffiths – Genome Medicine

Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa – Mun Fai Loke – Plos One

Review: Impact of maternal HIV exposure, feeding status, and microbiome on infant cellular immunity – Sonwabile Dzanibe – Journal of Leukocyte Biology

Review: Inherited nongenetic influences on the gut microbiome and immune system – Kathryn A. Knoop – Birth Defects Research

New insights into porcine milk N-glycome and the potential relation with offspring gut microbiome – Chunlong Mu – Journal of Proteome Research

Unraveling gut microbiota in Parkinson’s disease and atypical parkinsonism – Michela Barichella – Movement Disorders

Fecal SCFAs and SCFA-producing bacteria in gut microbiome of human NAFLD as a putative link to systemic T-cell activation and advanced disease – Monika Rau – United European Gastroenterology Journal

Skin microbiome

A tryptophan metabolite of the skin microbiota attenuates inflammation in atopic dermatitis via the aryl hydrocarbon receptor – Jinlei Yu – The Journal of Allergy and Clinical Immunology

Nasal microbiome

Competition among nasal bacteria suggests a role for siderophore-mediated interactions in shaping the human nasal microbiota – Reed M. Stubbendieck – Applied and Environmental Microbiology

Plant Microbiome

Metabolic niches in the rhizosphere microbiome: New tools and approaches to analyse metabolic mechanisms of plant-microbe nutrient exchange – Richard P Jacoby – Journal of Experimental Botany

Animal experiments

Chronic stress-induced gut dysfunction exacerbates Parkinson’s disease phenotype and pathology in a rotenone-induced mouse model of Parkinson’s disease – Hemraj B.Dodiya – Neurobiology of Disease

Ketamine interactions with gut-microbiota in rats: relevance to its antidepressant and anti-inflammatory properties – Bruk Getachew – BMC Microbiology

Dietary l-Tryptophan Supplementation Enhances the Intestinal Mucosal Barrier Function in Weaned Piglets: Implication of Tryptophan-Metabolizing Microbiota – Haiwei Liang – International Journal of Molecular Science

In Vivo Effects of Einkorn Wheat (Triticum monococcum) Bread on the Intestinal Microbiota, Metabolome, and on the Glycemic and Insulinemic Response in the Pig Model – Francesca Barone – Nutrients

Diet-Independent Correlations between Bacteria and Dysfunction of Gut, Adipose Tissue, and Liver: A Comprehensive Microbiota Analysis in Feces and Mucosa of the Ileum and Colon in Obese Mice with NAFLD – Eveline Gart – International Journal of Molecular Science

Abnormality in Maternal Dietary Calcium Intake During Pregnancy and Lactation Promotes Body WEIGHT gain by Affecting the Gut Microbiota in Mouse Offspring – Ping Li – Molecular Nutrition Food Research

Bilberry anthocyanin extract promotes intestinal barrier function and inhibits digestive enzyme activity by regulating the gut microbiota in aging rats – Jing Li – Food and Function

The gut microbiome is required for full protection against acute arsenic toxicity in mouse models – Michael Coryell – Nature Communications

Gut microbiota was modulated by moxibustion stimulation in rats with irritable bowel syndrome – Xiaomei Wang – Chinese Medicine

Bioinformatics

Rapid analysis of metagenomic data using signature-based clustering – Timothy Chappell – BMC Bioinformatics

Nonlinear expression and visualization of nonmetric relationships in genetic diseases and microbiome data – Xianchao Zhu – BMC Bioinformatics

Coupled dynamics of intestinal microbiome and immune system—A mathematical study – Akane Hara – Journal of Theoretical Biology

An adaptive microbiome α-diversity-based association analysis method – Hyunwook Koh – Scientific Reports

Good morning everyone. Today’s digest will cover recent studies focusing on the diet derived changes in the gut microbiome, the role of gut microbiome on brain health, inflammatory responses, autism, cystic fibrosis, hepatic steatosis using animal experiments, and reviews highlight the tumor genomics along with the microbiome and secretome as a new strategy in colorectal cancer. Enjoy reading.

General microbiome

Review: Is microbiome a target for the management of allergy associated diseases in children? – Ribaldone DG – European Review for Medical and Pharmacological Sciences

Review: Integrating tumor genomics into studies of the microbiome in colorectal cancer – Michael B Burns – Gut Microbes

Gut microbiome

Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota – Alexandra R.Lobach – Food and Chemical Toxicology

Review: Analysing the Secretome of Gut Microbiota as the Next Strategy For Early Detection of Colorectal Cancer – Putri‐Intan‐Hafizah Megat Mohd Azlan – Proteomics

Review: Bottoms up: the role of gut microbiota in brain health – Nina Radisavljevic – Environmental Microbiology

Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals – E. Angelakis – New Microbes and New Infections

Comparative Microbiome Signatures and Short-Chain Fatty Acids in Mouse, Rat, Non-human Primate, and Human Feces – Ravinder Nagpal – Frontiers in Microbiology

Synergistic convergence of microbiota-specific systemic IgG and secretory IgA – Jehane Fadlallah – The Journal of Allergy and Clinical Immunology

Water and extremophile microbiome

Microbial community composition and diversity in the Indian Ocean deep sea REY-rich muds – Shuyan Wang – PLOS One

Animal experiments

Following spinal cord injury, PDE4B drives an acute, local inflammatory response and a chronic, systemic response exacerbated by gut dysbiosis and endotoxemia – Scott A.Myer – Neurobiology of Disease

The Acute Influence of Acid Suppression with Esomeprazole on Gastrointestinal Microbiota and Brain Gene Expression Profiles in a Murine Model of Restraint Stress – RobertMacLaren – Neuroscience

Microbial communities in swine lungs and their association with lung lesions – Tao Huang – Microbial Biotechnology

Report: Gut microbial compositions mirror caste‐specific diets in a major lineage of social insects – Saria Otani – Environmental Microbiology Reports

Diet‐Induced Dysbiosis and Genetic Background Synergize With Cystic Fibrosis Transmembrane Conductance Regulator Deficiency to Promote Cholangiopathy in Mice – Dominique Debray – Hepatology Communications

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

Amelioration of hepatic steatosis is associated with modulation of gut microbiota and suppression of hepatic miR-34a in Gynostemma pentaphylla (Thunb.) Makino treated mice – Ning Jia – Nutritiion and Metabolism

Isolated Rearing at Lactation Increases Gut Microbial Diversity and Post-weaning Performance in PigsIsolated Rearing at Lactation Increases Gut Microbial Diversity and Post-weaning Performance in Pigs – Tsungcheng Tsai – Frontiers in Microbiology

Echinococcus granulosus Infection Results in an Increase in Eisenbergiella and Parabacteroides Genera in the Gut of Mice – Jianling Bao – Frontiers in Microbiology

Bioinformatics

Evaluation of metabolite-microbe correlation detection methods – YijunYou – Analytical Biochemistry

Microbes in News

Gut bacteria link to immunotherapy sparks interest – Brian Owens – Nature Biotechnology

Today’s microbiome digest will have more on gut microbiome, animal experiments along with one method DiTaxa for host phenotype and biomarker detection. Enjoy reading.

 General microbiome

Pre-transplant recovery of microbiome diversity without recovery of the original microbiome – Armin Rashidi – Bone Marrow Transplantation

Review: Importance of gut microbiota in obesity – Isabel Cornejo-Pareja – European Journal of Clinical Nutrition

Gut Microbiome and Plasma Microbiome-Related Metabolites in Patients With Decompensated and Compensated Heart Failure – Tomohiro Hayashi – Circulation Journal

Review: The lung and gut microbiome: what has to be taken into consideration for cystic fibrosis? – Geneviève Héry-Arnaud – Journal of Cystic Fibrosis

Gut microbiome

Impacts of dietary silver nanoparticles and probiotic administration on the microbiota of an in-vitro gut model – Cristina Cattò – Environmental Pollution

The Gut Microbiome: A Difficult Target for Translational Studies of Clostridium Difficile Colonization – Richard Kellermayer – Journal of Pediatric Gastroenterology and Nutrition

Altered gut microbiota after traumatic splenectomy is associated with endotoxemia – Hua Zhu – Emerging Microbes & Infections

Gut Microbiota Modulates Interactions Between Polychlorinated Biphenyls and Bile Acid Homeostasis – Sunny Lihua Cheng – Toxicological Sciences

The intestinal microbiome and its relevance for functionality in older persons – Andrea Ticinesi – Current Opinion in Clinical Nutrition and Metabolic Care

Gut Microbiota Disruption in Septic Shock Patients: A Pilot Study – You-Dong Wan – Medical Science Monitor

Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants – Bing Ma – Frontiers in Microbiology

Review: Microbial impact on cholesterol and bile acid metabolism: current status and future prospects – Aicha Kriaa – Journal of Lipid Research

Respiratory microbiome

Characterising the respiratory microbiome – Rebecca L. Watson – European Respiratory Journal

Vaginal microbiome

Characterization of vaginal microbiota in Thai women – Auttawit Sirichoat – PeerJ

Normal vaginal microbiome in women with primary Sjögren’s syndrome-associated vaginal dryness – van der Meulen TA – Annals of the Rheumatic Diseases

Animal experiments

On the role of corticosterone in behavioral disorders, microbiota composition alteration and neuroimmune response in adult male mice subjected to maternal separation stress – HosseinAmini-Khoei – International Immunopharmacology

Insights into a Possible Mechanism Underlying the Connection of Carbendazim-Induced Lipid Metabolism Disorder and Gut Microbiota Dysbiosis in Mice – Cuiyuan Jin – Toxicological Sciences

General Anesthesia Alters the Diversity and Composition of the Intestinal Microbiota in Mice – Mara A. Serbanescu – Anesthesia & Analgesia

Lactobacillus helveticus KLDS1.8701 alleviates D-galactose-induced aging by regulating Nrf-2 and gut microbiota in mice – Bailiang Li – Food and Function

The Host Microbiota Contributes to Early Protection Against Lung Colonization by Mycobacterium tuberculosis – Alexia Dumas – Frontiers in Immunology

Cesarean Section Induces Microbiota-Regulated Immune Disturbances in C57BL/6 Mice – Line Fisker Zachariassen – The Journal of Immunology

Bioinformatics

DiTaxa: Nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection – Ehsaneddin Asgari – Bioinformatics