November 30, 2019

Have a nice weekend! In this Digest, we have a set of reviews about the gut-brain axis, covering associations between microbiota and neurological diseases, as well as a set of reviews about the connection between the microbiome and the immune system. We have also a paper about the microbiome from people living in high-altitude environments, and of course, several papers more. 

 

Human and General Microbiome

Gut microbiota composition in Himalayan and Andean populations and its relationship with diet, lifestyle and adaptation to the high-altitude environment – Andrea Quagliariello – Journal of Anthropological Sciences

Microbiological evidences for gastric cardiac microflora dysbiosis inducing the progression of inflammation – Ruijing Yan – Journal of Gastroenterology and Hepatology

Review: Targeting the gut microbiota for the treatment of irritable bowel syndrome – Charles C. Herndon – The Kaohsiung Journal of Medical Sciences

Review: The Gut Microbiome and Treatment-Resistance in Schizophrenia – Mary V. Seeman – Psychiatric Quarterly

Review: The Role of the Gut Microbiota in the Pathogenesis of Parkinson’s Disease – Dongming Yang – Frontiers in Neurology

Editorial: Interactions of the microbiota with the mucosal immune system – Calum C. Bain – Immunology

Review: Understanding immune-microbiota interactions in the intestine – Philip P. Ahern – Immunology

Review: The interaction of intestinal microbiota and innate lymphoid cells in health and disease throughout life – Stephanie C. Ganal‐Vonarburg – Immunology

Review: Immunological mechanisms underpinning faecal microbiota transplantation for the treatment of inflammatory bowel disease – M. N. Quraishi – Clinical and Experimental Immunology

Review: Population Genetics in the Human Microbiome – Nandita R. Garud – Trends in Genetics

Review: Gut Microbiota And The Use Of Probiotics In Constipation In Children And Adolescents: Systematic Review – Daiane Oliveira Vale San Gomes – Revista Paulista de Pediatria

Review: The gut microbiota modulates both browning of white adipose tissue and the activity of brown adipose tissue – José María Moreno-Navarrete – Reviews in Endocrine and Metabolic Disorders

Decoding Microbiome Research for Clinical Psychiatry – Jane A. Foster – The Canadian Journal of Psychiatry

Lactobacillus iners Is Associated with Vaginal Dysbiosis in Healthy Pregnant Women: A Preliminary Study – Nengneng Zheng – BioMed Research International

Human Endometrial Microbiota at Term of Normal Pregnancies – Claudia Leoni – Genes (MDPI)

Helicobacter pylori Infection Aggravates Dysbiosis of Gut Microbiome in Children With Gastritis – Lu Yang – Frontiers in Cellular and Infection Microbiology

The Effect of Gut Microbiome Composition on Human Immune Responses: An Exploration of Interference by Helminth Infections – Ivonne Martin – Frontiers in Genetics

Metagenome-wide association study of the alterations in the intestinal microbiome composition of ankylosing spondylitis patients and the effect of traditional and herbal treatment – RunYue Huang – Journal of Medical Microbiology 

Gut Microbiota and Cardiometabolic Risk Factors in Hemodialysis Patients: A Pilot Study – Annabel Biruete – Topics in Clinical Nutrition

Habitual animal fat consumption in shaping gut microbiota and microbial metabolites – Yi Wan – Food and Function

 

Animal Microbiome and Animal Experiments

Division of labor in honey bee gut microbiota for plant polysaccharide digestion – Hao Zheng – PNAS

Exploring interactions between xenobiotics, microbiota, and neurotoxicity in zebrafish – Luísa B. Bertotto – NeuroToxicology

The Skin Microbiota of Eleutherodactylus Frogs: Effects of Host Ecology, Phylogeny, and Local Environment – Liza Garcia-Recinos – Frontiers in Microbiology

The intestinal microbiota of lake anchovy varies according to sex, body size, and local habitat in Taihu Lake, China – Min Jiang – Microbiology Open

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition – Nicholas M. Fountain‐Jones – Journal of Animal Ecology

Immunodeficiency Promotes Adaptive Alterations of Host Gut Microbiome: An Observational Metagenomic Study in Mice – Shuyu Zheng – Frontiers in Microbiology

Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics – Jie Han – Scientific Reports

Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome – Rafael J. Vivero – Scientific Reports

Ochratoxin A induces liver inflammation: involvement of intestinal microbiota – Wence Wang – Microbiome

Toxicity, Pharmacokinetics, and Gut Microbiome of Oral Administration of Sesterterpene MHO7 Derived from a Marine Fungus – Wei Tian – Marine Drugs

 

Bioinformatics

AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data –  M. Shaffer – BMC Bioinformatics

Managing batch effects in microbiome data – Yiwen Wang – Briefings in Bioinformatics

Review: Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities – Duo Jiang – Frontiers in Genetics

 

Methods

Exploring the chemical space of the human microbiome – Lei Tang – Nature Methods

 

Other

Microbiome Response to Hot Water Treatment and Potential Synergy With Biological Control on Stored Apples – Birgit Wassermann – Frontiers in Microbiology 

Year in Review: Big data and tiny proteins: shining a light on the dark corners of the gut microbiome – Suzanne Devkota – Nature Reviews Gastroenterology & Hepatology 

 

November 26, 2019

Have a nice day! Today in this Digest, we have papers about the microbiome and colorectal carcinoma and autism spectrum disorder, as well as studies about skin microbiota. We have also a set of papers about the effect of diet or probiotics in different animal systems, as well as some studies in insects. 

 

Human and General Microbiome

Resistant starch: impact on the gut microbiome and health – Peter DeMartino – Current Opinion in Biotechnology

Mucosal cancer-associated microbes and anastomotic leakage after resection of colorectal carcinoma – Kosuke Mima – Surgical Oncology

Mycobacterial immunomodulation and viral manipulation of neuronal copper efflux in the setting of sporadic Parkinson’s disease: A multi – hit, outside – in hypothesis of its pathogenesis – George D.Vavougios – Medical Hypotheses

Specificity of gut microbiota in children with autism spectrum disorder in Slovakia and its correlation with astrocytes activity marker and specific behavioural patterns – A.Tomova – Physiology & Behavior

Small intestinal bacterial overgrowth is associated with Diarrhea-predominant irritable bowel syndrome by increasing mainly Prevotella abundance – Kang-Qi Wu – Scandinavian Journal of Gastroenterology 

Probiotics of Diverse Origin and Their Therapeutic Applications: A Review – Monika Yadav – Journal of the American College of Nutrition 

Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease – Shivani Kansal – Journal of Pediatric Gastroenterology and Nutrition

Dataset of the microbiome composition in skin lesions caused by lumpy skin disease virus via 16s rRNA massive parallel sequencing – Sören Hansen – Data in Brief 

Characterization of Skin Microbiome in Tinea Pedis – Xiaoping Liu – Indian Journal of Microbiology

Human Milk Microbiota: Transferring the Antibiotic Resistome to Infants – Lahari Das –  Indian Journal of Microbiology

Vertical selection for nuclear and mitochondrial genomes shapes gut microbiota and modifies risks for complex diseases – Youjie Zhang – Physiological Genomics

The relationship of gastric microbiota and Helicobacter pylori infection in pediatrics population – Ruixue Miao – Helicobacter

The impact of vitamin B12 deficiency on infant gut microbiota – Perran Boran – European Journal of Pediatrics

Novel Therapies for Treatment of Food Allergy – Sultan Albuhairi – Immunology and Allergy Clinics

Structural and Functional Bases of Genitourinary Syndrome of Menopause – A. K. Pichigina – Bulletin of Experimental Biology and Medicine

The role of bacteria and its derived metabolites in chronic pain and depression: Recent findings and research progress – Shan Li – International Journal of Neuropsychopharmacology

Microbial supernatants from Mobiluncus mulieris, a bacteria strongly associated with spontaneous preterm birth, disrupts the cervical epithelial barrier through inflammatory and miRNA mediated mechanisms – Carolynn M. Dude – Anaerobe

Overview of prospects for inflammation pathways in autism spectrum disorders – H.Turbé – L’Encéphale

 

Animal Microbiome and Animal Experiments

The effect of nitrite and sulfide on the antioxidant capacity and microbial composition of the intestines of red swamp crayfish, Procambarus clarkii – Kun Guo – Fish & Shellfish Immunology

Feed supplementation with inulin on broiler performance and meat quality challenged with Clostridium perfringens: Infection and prebiotic impacts – Andréia Guaragni – Microbial Pathogenesis

Strain specific stress-modulating effects of candidate probiotics: a systematic screening in a mouse model of chronic restraint stress – Lotta K. Stenman – Behavioural Brain Research

Effects of the solubility of yeast cell wall preparations on their potential prebiotic properties in dogs – Stephanie de Souza Theodoro – PLoS One

The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster – Gabrielle M. Solomon – PeerJ

Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies – Rittik Deb​ – PeerJ

Kestose supplementation exerts bifidogenic effect within fecal microbiota and increases fecal butyrate concentration in dogs – Kaori Ide – Journal of Veterinary Medical Science

Interactions between host and gut microbiota in domestic pigs: a review – Yadnyavalkya Patil – Gut Microbes

Absorptive transport of amino acids by the rat colon – Yuxin Chen – Gastrointestinal and Liver Physiology

Video: Visualization of Candida albicans in the Murine Gastrointestinal Tract Using Fluorescent In Situ Hybridization – Jessica N. Witchley – JoVE

Video: Infecting Mice with Malassezia spp. to Study the Fungus-Host Interaction – Florian Sparber – JoVE

 

Plant and Soil Microbiome

Assisted phytoremediation of chromium spiked soils by Sesbania Sesban in association with Bacillus xiamenensis PM14: A biochemical analysis – Bashir Ud Din – Plant Physiology and Biochemistry

Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds – Sanderson Tarciso Pereira de Sousa – Ecotoxicology and Environmental Safety

November 19, 2019

Have a nice Tuesday! Today, in this Digest we have several papers about the microbiome and respiratory health.  We have also papers about the detection of archaeal species in caries biofilm, microbiome and cancer, and microbiome changes by the use of fish oil and their effect on (TMAO)-exacerbated atherogenesis. And of course, more papers… 

 

Human and General Microbiome

Minireview: The Microbiome, Malignant Fungating Wounds, and Palliative Care – Mridula Vardhan – Frontiers in Cellular and Infection Microbiology

Gut microbiota: from the forgotten organ to a potential key player in the pathology of Alzheimer disease – Dong-oh Seo – The Journals of Gerontology

Presence of Archaea in dental caries biofilms – Naile Dame-Teixeira – Archives of Oral Biology

Increased Moraxella and Streptococcus following severe bronchiolitis is associated with recurrent wheezing – Jonathan M. Mansbach  – Journal of Allergy and Clinical Immunology

Composition and Diversity of Bacterial Community on the Ocular Surface of Patients With Meibomian Gland Dysfunction – Xiaojin Dong – Investigative Ophthalmology & Visual Science 

Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia – Heng Choon Cheong – Plos One

Competition Among Gardnerella Subgroups From the Human Vaginal Microbiome – Salahuddin Khan – Frontiers in Cellular and Infection Microbiology

Review: Potential clinical utility of multiple target quantitative polymerase chain reaction (qPCR) array to detect microbial pathogens in patients with chronic obstructive pulmonary disease (COPD) – Hannah E. O’Farrell – Journal of Thoracic Disease 

Review: COPD and the gut-lung axis: the therapeutic potential of fibre – Annalicia Vaughan – Journal of Thoracic Disease 

Review: Chronic obstructive pulmonary disease (COPD) and lung cancer: common pathways for pathogenesis – Brielle A. Parris – Journal of Thoracic Disease 

The Vaginal Community State Types Microbiome-Immune Network as Key Factor for Bacterial Vaginosis and Aerobic Vaginitis – Francesco De Seta – Frontiers in Microbiology

Gut Microbiota in Bipolar Depression and Its Relationship to Brain Function: An Advanced Exploration – Qiaoqiao Lu – Frontiers in Psychiatry

Fish oil is more potent than flaxseed oil in modulating gut microbiota and reducing trimethylamine-N-oxide (TMAO)-exacerbated atherogenesis – Zouyan He – Journal of Agricultural and Food Chemistry 

Characterization of gut microbiota in children with pulmonary tuberculosis – Weiran Li – BMC Pediatrics

Editorial: Bugs, Drugs, and Shrugs – James T. Rosenbaum – Arthritis and Rheumatology

Opinion: Harnessing the Microbiome for Pancreatic Cancer Immunotherapy – Gerardo A. Vitiello – Trends in Cancer

 

Animal Microbiome / Animal Experiments

Review: Maternal imprinting of the neonatal microbiota colonization in intrauterine growth restricted piglets: a review – Lili Jiang – Journal of Animal Science and Biotechnology

Colonization of the gut microbiota of honey bee (Apis mellifera) workers at different developmental stages – Xiang Dong – Microbiological Research 

Effects of oral exposure to titanium dioxide nanoparticles on gut microbiota and gut-associated metabolism in vivo – Zhangjian Chen – Nanoscale

Sex, Age, and Bacteria: How the Intestinal Microbiota Is Modulated in a Protandrous Hermaphrodite Fish – M. Carla Piazzon – Frontiers in Microbiology

Dynamic Changes in the Microbiome and Mucosal Immune Microenvironment of the Lower Respiratory Tract by Influenza Virus Infection – Liming Gu – Frontiers in Microbiology

Fuzhuan brick tea attenuates high-fat diet-induced obesity and associated metabolic disorders by shaping gut microbiota – Dongmin Liu – Journal of Agricultural and Food Chemistry 

 

Plant Microbiome

Rapid Detection of Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli in Common Bean by Loop-Mediated Isothermal Amplification – Bruna Alicia Rafael de Paiva – Plant Disease

Beneficial Plant Microorganisms Affect the Endophytic Bacterial Communities of Durum Wheat Roots as Detected by Different Molecular Approaches – Monica Agnolucci –  Frontiers in Microbiology

 

Methods

Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations – Doratha A. Byrd – Plos One

 

Bioinformatics

Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities – Laura M Zingaretti – Bioinformatics

 

Other papers

Antibiotic exposure and risk of Parkinson’s disease in finland: A nationwide case-control study – Tuomas H. Mertsalmi – Movement Disorders

 

November 12, 2019

Have a nice day! Today we have reviews about the “hologenome” concept, the influence of stress on IBD flares in children and adults and microbiome and liver disease. In addition, we have articles about the effect of UV light on skin microbiota, alligator microbiome, and more!

 

Human and General Microbiome

Perspective: The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis – Adena Collens – Molecular and Developmental Evolution

Review: Stress Triggers Flare of Inflammatory Bowel Disease in Children and Adults – Yue Sun – Frontiers in Pediatrics

Review: Current US Food and Drug Administration-Approved Pharmacologic Therapies for the Treatment of Irritable Bowel Syndrome with Diarrhea – Darren M. Brenner – Advances in Therapy

Review: Microbiome Modulation in Liver Disease – Eamonn M.M. Quigley – Clinical Liver Disease

Viewpoint: How the joint study of the microbiota and metabolites in different body fluids may aid in the identification of novel disease mechanisms – Jordi Mayneris‐Perxachs – The FEBS Journal

Microbial Metabolite Signaling Is Required for Systemic Iron Homeostasis – Nupur K. Das – Cell Metabolism

Characteristics of Gut Microbiota in Patients With Rheumatoid Arthritis in Shanghai, China – Yang Sun – Frontiers in Cellular and Infection Microbiology

Using compositional principal component analysis to describe children’s gut microbiota in relation to diet and body composition – Claudia Leong – The American Journal of Clinical Nutrition

Skin Exposure to Narrow Band Ultraviolet (UVB) Light Modulates the Human Intestinal Microbiome – Else S. Bosman – Frontiers in Microbiology

The Therapeutic Effect of 1,8-Cineol on Pathogenic Bacteria Species Present in Chronic Rhinosinusitis – Matthias Schürmann – Frontiers in Microbiology

Potential correlation between dietary fiber suppresses microbial conversion of choline to trimethylamine and formation of methylglyoxal – Qian Li – Journal of Agricultural and Food Chemistry

 

Animal Microbiome

Host-associated microbiomes drive structure and function of marine ecosystems – Laetitia G. E. Wilkins – PLoS Biology

Intake of Watermelon or Its Byproducts Alters Glucose Metabolism, the Microbiome, and Hepatic Proinflammatory Metabolites in High-Fat-Fed Male C57BL/6 J Mice – Alexandra R Becraft – The Journal of Nutrition

Mixed mode bacterial transmission in the common brooding coral Pocillopora acuta – Katarina Damjanovic – Environmental Microbiology

The Effect of Milk Replacer Composition on the Intestinal Microbiota of Pre-ruminant Dairy Calves – James Badman – Frontiers in Veterinary Sciences

Metagenomics Reveals Seasonal Functional Adaptation of the Gut Microbiome to Host Feeding and Fasting in the Chinese Alligator – Ke-Yi Tang – Frontiers in Microbiology

A Short-Term Feeding of Dietary Casein Increases Abundance of Lactococcus lactis and Upregulates Gene Expression Involving Obesity Prevention in Cecum of Young Rats Compared With Dietary Chicken Protein – Fan Zhao – Frontiers in Microbiology

Microbiota assessment across different developmental stages of Dermacentor silvarum (Acari: Ixodidae) revealed stage-specific signatures – Zhang Ruiling – Ticks and Tick-borne Diseases

 

Food Microbiome

Tracking bacteriome variation over time in Listeria monocytogenes-positive foci in food industry – Pedro Rodríguez-López – International Journal of Food Microbiology

 

Environmental Microbiome

Response mechanism of microbial community to the environmental stress caused by the different mercury concentration in soils – Lei Wang – Ecotoxicology and Environmental Safety

 

Other papers

The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions – Eoghan M. Smyth – Frontiers in Microbiology 

 

Methods and Techniques

Review: A Bioinformatics Guide to Plant Microbiome Analysis – Rares Lucaciu – Frontiers in Plant Sciences

Drug Discovery and Repurposing Inhibits a Major Gut Pathogen-Derived Oncogenic Toxin – Paul Metz – Frontiers in Cellular and Infection Microbiology

Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study – Jinbing Bai – JMIR Medical Informatics

Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia – So Nakagawa – Clinical and Translational Immunology 

November 5, 2019

Today, in this brief digest:  microbiome and metabolic signatures in IBS, the influence of US immigration on antimicrobial resistance gene spreading, the importance of microbiota delivery, the potential role of the microbiome in head and neck cancer oncogenesis, and more other papers. Have a nice day!

 

Human or General Microbiome

The internationalization of human microbiome research – Ana Maria Porras – Current Opinion in Microbiology 

Identification of Gut Microbiota and Metabolites Signature in Patients With Irritable Bowel Syndrome – Shengtao Zhu – Frontiers in Cellular and Infection Microbiology 

Incidence of Bloodstream Infections, Length of Hospital Stay, and Survival in Patients With Recurrent Clostridioides difficile Infection Treated With Fecal Microbiota Transplantation or Antibiotics: A Prospective Cohort Study – Gianluca Ianiro – Annals of Internal Medicine

Delivery to the gut microbiota: A rapidly proliferating research field – Adi Seifert – Advances in Colloid and Interface Science

Potential role of microbiome in oncogenesis, outcome prediction and therapeutic targeting for head and neck cancer – Ester Orlandi – Oral Oncology

Alterations in Oral Microbiota in HIV are Related to Decreased Pulmonary Function – Libing Yang – American Journal of Respiratory and Critical Care Medicine

Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life – Marta Reyman – Nature Communication

Periodontopathogenic microbiota, infectious mechanisms and preterm birth: analysis with structural equations (cohort-BRISA) – Elisa Miranda Costa – Archives of Gynecology and Obstetrics

Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension – Francine Z. Marques – Hypertension

US immigration is associated with rapid and persistent acquisition of antibiotic resistance genes in the gut – Quentin Le Bastard – Clinical Infectious Diseases

 

Beneficial compounds and microbes

Changes in stool frequency following chicory inulin consumption, and effects on stool consistency, quality of life and composition of gut microbiota – Anthony W. Watson – Food Hydrocolloids

Prophages in Lactobacillus reuteri are associated with fitness trade-offs but can increase competitiveness in the gut ecosystem – Jee-Hwan Oh – Applied and Environmental Microbiology

 

Animal Microbiome / Animal Experiments

Effect of Metformin on Short-Term High-Fat Diet-Induced Weight Gain and Anxiety-Like Behavior and the Gut Microbiota – Shuqin Ji – Frontiers in Endocrinology 

Both gut microbiota and cytokines act to atherosclerosis in ApoE-/- mice – Qiuxia Liu – Microbial Pathogenesis 

The Effect of Clostridium butyricum on Gut Microbiota, Immune Response and Intestinal Barrier Function During the Development of Necrotic Enteritis in Chickens – Ting Huang – Frontiers in Microbiology

Lactic Acid Treatment of Cereals and Dietary Phytase Modified Fecal Microbiome Composition Without Affecting Expression of Virulence Factor Genes in Growing Pigs – Jutamat Klinsoda – Frontiers in Microbiology

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus) – Corey C. Holt – The ISME Journal 

An antibiotic depleted microbiome drives severe Campylobacter jejuni-mediated Type 1/17 colitis, Type 2 autoimmunity and neurologic sequelae in a mouse model – Phillip T. Brooks – Journal of Neuroimmunology

 

Environmental Microbiome

Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study – Xiaole Yin – Environment International

 

Bioinformatics

Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data – Nidhi Shah – Frontiers in Genetics

Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families – Yan Wang – Genome Biology

 

Techniques

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing – Shailesh K. Shahi – JoVE

Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study – Gabriela Guimaraes Sousa Leite – BMC Microbiology

September 26, 2019

Have a nice day! Today, in this digest we have a good number of papers, including those associated with beneficial microbes, compounds, and interventions. Some highlights: host-microbiome evolution, microbiome and urinary tract infections, the first reported bloodstream infection caused by gut-habiting Prevotella species, microbiome activity in halitosis, and more! Enjoy.   

 

General or Human Microbiome

The role of multilevel selection in host microbiome evolution – Simon van Vliet – PNAS

Review: Diagnosis of Urinary Tract Infection in the Neuropathic Bladder: Changing the Paradigm to Include the Microbiome – Catherine S. Forster – Topics in Spinal Cord Injury Rehabilitation 

Review: A critical review on diet-induced microbiota changes and cardiovascular diseases – Muthukumaran Jayachandran – Critical Reviews in Food Science and Nutrition 

Review: Microbiota: a novel regulator of pain – Manon Defaye – Journal of Neural Transmission

Relationship of tongue coating microbiome on volatile sulfur compounds in healthy and halitosis adults – Wei Ye – Journal of Breath Research

An Infectious Diseases Perspective on Fecal Microbiota Transplantation for Clostridioides difficile Infection in Children – Jillian M Cotter – Journal of the Pediatric Infectious Diseases Society

First bloodstream infection caused by Prevotella copri in a heart failure elderly patient with Prevotella-dominated gut microbiota: a case report – Patrizia Posteraro – Gut Pathogens

Pain regulation by gut microbiota: molecular mechanisms and therapeutic potential – Ran Guo – British Journal of Anaesthesia

The Dysbiosis and Inter-Kingdom Synergy Model in Oropharyngeal Candidiasis, a New Perspective in Pathogenesis – Martinna Bertolini – Journal of Fungi

Microbiome Influence in the Pathogenesis of Prion and Alzheimer’s Diseases – Valeria D’Argenio – International Journal of Molecular Sciences

Protein Intake at Twice the RDA in Older Men Increases Circulatory Concentrations of the Microbiome Metabolite Trimethylamine-N-Oxide (TMAO) – Sarah M. Mitchell – Nutrients

Potential Strategies in the Prevention of Nonsteroidal Anti-inflammatory Drugs-Associated Adverse Effects in the Lower Gastrointestinal Tract – Chuan-Guo Guo – Gut and Liver

 

Composition of gut microbiota of children and adolescents with perinatal HIV infection taking antiretroviral therapy in Zimbabwe – Trym T Flygel – The Journal of Infectious Diseases

Gut Microbiome in Psoriasis is Perturbed Differently During Secukinumab and Ustekinumab Therapy and Associated with Response to Treatment – Nai-Lun Yeh – Clinical Drug Investigation

The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants – Masaru Tanaka – Gut Microbes

 

Animal Microbiome

Food Preservatives Induce Proteobacteria Dysbiosis in Human-Microbiota Associated Nod2-Deficient Mice – Lucia Hrncirova – Microorganisms

Maternal Dietary Protein Intake Influences Milk and Offspring Gut Microbial Diversity in a Rat (Rattus norvegicus) Model –  Matthew F. Warren – Nutrients

Microbiota, Gut Health and Chicken Productivity: What Is the Connection? – Juan M. Diaz Carrasco – Microorganisms

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets – Raphaële Gresse – Microorganisms 

Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring – Pedro Soares-Castro – Scientific Reports

Core gut microbial communities are maintained by beneficial interactions and strain variability in fish – Fotini Kokou – Nature Microbiology

Beneficial Microbes and Compounds

Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly – Kerry L. Ivey – mBio

Oral Administration of β-Glucan and Lactobacillus plantarum Alleviates Atopic Dermatitis-like Symptoms – In Sung Kim – Journal of Microbiology and Biotechnology

Protective Effect of Probiotic Bacteria and Estrogen in Preventing HIV-1-Mediated Impairment of Epithelial Barrier Integrity in Female Genital Tract – Sara Dizzell – Cells (MPDI)

Fish Oil, but Not Olive Oil, Ameliorates Depressive-Like Behavior and Gut Microbiota Dysbiosis in Rats under Chronic Mild Stress – Te-Hsuan Tung – Biomolecules

The Potential Impact of Probiotics on the Gut Microbiome of Athletes – Laura Wosinska – Nutrients

Royal Jelly and Its Components Promote Healthy Aging and Longevity: From Animal Models to Humans – Hiroshi Kunugi – International Journal of Molecular Sciences

Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond – Carrie A. M. Wegh – International Journal of Molecular Sciences

Antifungal and Antivirulence Activity of Vaginal Lactobacillus Spp. Products against Candida Vaginal Isolates – Camilla Itapary dos Santos – Pathogens

Metabolic and Vascular Effect of the Mediterranean Diet – Antonino Tuttolomondo – International Journal of Molecular Sciences

 

Environmental Microbiome

Unveiling resistome profiles in the sediments of an Antarctic volcanic island – V.B. Centurion – Environmental Pollution

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea – Nojood A. Aalismail – Scientific Reports

 

Bioinformatics

The EFI Web Resource for Genomic Enzymology Web Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways – Rémi Zallot – Biochemistry

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification – Florian P Breitwieser – Biochemistry

 

Methods

Review: Common principles and best practices for engineering microbiomes – Christopher E. Lawson – Nature Reviews Microbiology

Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome – Oskar Hickl – Microorganisms

Optimizing bacterial DNA extraction in urine – Matthew M. Munch – PLoS One

 

September 20, 2019

Have a nice day! In this digest, an interesting study about the relationship between peripheral serotonin synthesis and host glucose homeostasis, as well as another study showing the long-term maintained high levels of Proteobacteria in Crohn’s disease. And, of course, more papers!

 

Human and General Microbiome

Are we Ready for a “Microbiome-Guided Behaviour” Approach? – Andrea Lavazza – Cambridge Quarterly of Healthcare Ethics

The gut microbiome regulates host glucose homeostasis via peripheral serotonin – Alyce M. Martin – PNAS

Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis – M. K. Vester-Andersen – Scientific Reports

The Gut Microbiome and Pediatric Cancer: Current Research and Gaps in Knowledge – Roma Bhuta – JNCI Monographs

Time to test antibacterial therapy in Alzheimer’s disease – Francesco Panza – Brain

Discrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities – Qiang Zeng – Scientific Reports

Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples – Sonia Tarallo – mSystems

Analysis of gut microbiome, nutrition and immune status in autism spectrum disorder: a case-control study in Ecuador – María Fernanda Zurita – Gut Microbes 

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – BJOG

Development of an Index Score for Intestinal Inflammation-Associated Dysbiosis Using Real-World Stool Test Results – Lihong Chen – Digestive Diseases and Sciences

Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome – Carrie E. Jung – Scientific Reports

Dysbiotic microbiota in autistic children and their mothers: persistence of fungal and bacterial wall-deficient L-form variants in blood – N. Markova – Scientific Reports

Features of Fecal and Colon Microbiomes Associate With Responses to Biologic Therapies for Inflammatory Bowel Diseases: a Systematic Review – Maria Manuela Estevinho – Clinical Gastroenterology and Hepatology

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients – Anuradha Ravi – Microbial Genomics

Complex interactions between the microbiome and cancer immune therapy – Drew J. Schwartz – Critical Reviews in Clinical Laboratory Sciences

Disentangling the effect of host genetics and gut microbiota on resistance to an intestinal parasite – Bruno Faivre – International Journal for Parasitology

Small talk: microbial metabolites involved in the signaling from microbiota to brain – Giorgia Caspani – Current Opinion in Pharmacology

Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients – Solveig Tangedal – PLoS One

 

Animal Microbiome / Animal Experiments

Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster – Seth M. Rudman – PNAS

Abnormal composition of gut microbiota is associated with resilience versus susceptibility to inescapable electric stress – Kai Zhang – Translational Psychiatry

Adenovirus infection is associated with altered gut microbial communities in a non-human primate – Wasimuddin – Scientific Reports

 

Beneficial Microbes and Compounds

Honey Polyphenols Ameliorate DSS-induced Ulcerative Colitis Via Modulating Gut Microbiota in Rats – Haoan Zhao – Molecular Nutrition and Food Research

ω-3 PUFAs Alleviate High-fat Diet Induced Circadian Intestinal Microbes Dysbiosis – Lifeng Gui – Molecular Nutrition and Food Research

Additional Candida albicans administration enhances the severity of dextran sulfate solution induced colitis mouse model through leaky gut-enhanced systemic inflammation and gut-dysbiosis but attenuated by Lactobacillus rhamnosus L34 – Wimonrat Panpetch – Gut Microbes

Equol: A Bacterial Metabolite from The Daidzein Isoflavone and Its Presumed Beneficial Health Effects –  Baltasar Mayo – Nutrients

Dietary cranberry suppressed colonic inflammation and alleviated gut microbiota dysbiosis in dextran sodium sulfate-treated mice – Xiaokun Cai – Food and Function

 

Food Microbiome

Deciphering the microbiome shift during fermentation of medicinal plants – Martina Köberl – Scientific Reports

 

Plant Microbiome

The aeroponic rhizosphere microbiome: community dynamics in early succession suggest strong selectional forces – Jennifer W. Edmonds – Antonie van Leeuwenhoek

 

Extremophiles

A shared core microbiome in soda lakes separated by large distances – Jackie K. Zorz – Nature Communications

 

Methods

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method – Sukithar K. Rajan – PLoS One

Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing – Emma E. Ilett – Scientific Reports