December 6, 2019

Today’s post is about metabolic networks of the human gut microbiota with host, how aging affects microbial world in humans, microbiome in honey bee and lifestyle dependent gut microbiota gradients in diverse Indian population. Have a nice weekend!

General microbiome

Review: Metabolic networks of the human gut microbiota – Susannah Selber-Hnatiw – Microbiology

Review: Cannabinoids and the Microbiota‐Gut‐Brain‐Axis: Emerging Effects of Cannabidiol and Potential Applications to Alcohol Use Disorders – Hollis C. Karoly – Alcoholism Clinical and Experimental Research

Review: The Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging – Oscar Salvador Barrera-Vázquez – Journal of Gerontology

Review: Nanotechnology intervention of the microbiome for cancer therapy – Wantong Song – Nature Nanotechnology

Commentary: Gut microbiome influences exercise response – Claire Greenhill – Nature Reviews Endocrinology

Human microbiome

Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma – Victor Tetz – Scientific Reports

Lifestyle induced microbial gradients: An Indian perspective – Rashmi Singh – Frontiers in Microbiology

Microbiota, type 2 diabetes and non-alcoholic fatty liver disease: protocol of an observational study – Benedetta M. Motta – Journal of Translational Medicine

Antibiotic exposure and the risk of colorectal adenoma and carcinoma: systematic review and meta‐analysis of observational studies – Leigh N. Sanyaolu – Colorectal Disease

Higher frequency of vertebrate‐infecting viruses in the gut of infants born to mothers with type 1 diabetes – Ki Wook Kim – Pediatric Diabetes

Animal experiments

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

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

The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera) – Michelle A. Taylor – PlosOne

Seven-day Green Tea Supplementation Revamps Gut Microbiome and Caecum/Skin Metabolome in Mice from Stress – Eun Sung Jung – Scientific Reports

Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonization travel – Raies A. Mir – PlosOne

Characterization of the cecal microbiome composition of Wenchang chickens before and after fattening – Zhen Tan – PlosOne

SOD1 deficiency alters gastrointestinal microbiota and metabolites in mice – Haruka Sagi – Experimental Gerontology

Plant, soil, root microbiome

Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere – Michael D. Jochum – PlosOne

Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing – Preshita S. Gadkari – FEMS Microbiology Ecology

Techniques

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces – Richard W. Hagan – American Journal of Physical Anthropology

Microbes in the news

How Microbiomes Affect Fear – Quanta Magazine

Rainforest Dwellers and Urbanites Have Consistently Different Microbiomes – Scientific American

Human Microbiome Modulators Market is Furbishing worldwide with Bayer, BioGaia, Chr. Hansen Holding, DowDuPont – News Description

December 4, 2019

Highlights: Microbiome of human milk, AMON to integrate microbiome and metabolome data, soil microbiomes, skin microbiome based news and many more!

General microbiome

The fight for glycans in reproductive tract microbial ecology – MIH Pishchany – AJOG

Microbiota, a Third Player in the Host–Plasmodium Affair – D Mukherjee – Trends in Parasitology

Pregnancy and early life

Baby’s First Microbes: The Microbiome of Human Milk – MC Collado – How Fermented Foods Feed a Healthy Gut Microbiota

Human respiratory microbiome

Anterior Nares Diversity and Pathobionts Represent Sinus Microbiome in Chronic Rhinosinusitis – ID Boeck – mSphere

Animal microbiome 

Next generation sequencing reveals significant variations in bacterial compositions across the gastrointestinal tracts of the Indian major carps, rohu (Labeo rohita), catla (Catla catla) and mrigal (Cirrhinus cirrhosis) – MJ Foysal – Letters in Applied Microbiology

Plant, root, and soil microbiome

Rewetting of three drained peatlands drives congruent compositional changes in pro- and eukaryotic microbiomes through environmental filtering – M Weil – bioRxiv

The influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation –  R Bartelme – bioRxiv

Rhizosphere: a home for human pathogens – R Sharma – Plant Biotic Interactions

Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes – SD Mandal – Environmental Monitoring and Assessment

Soil bacterial and fungal communities exhibit distinct long-term responses to disturbance in temperate forests – ED Osburn – Frontiers in Microbiology

Decomposition of mixtures of cover crop residues increases microbial functional diversity – SM Drost – Geoderma

Techniques

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

Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity – GS Watts – PLoS Computational Biology

Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes – BO Oyserman – bioRxiv

Microbes in the news

Korean beauty makers join the rush towards new skin gold mine of microbiome – Pulse

Mode of Delivery May Alter Microbiome, But Study Finds No Link to Later GI Issues – Gastro Endo News

Smart Skin care – Cosmetics Design Europe

The Dynamic Microbiome – Gen Eng News

microRNA Found in Gut Microbiome May Unlock Future Therapeutic Approach for MS – Multiple Sclerosis News Today

A Matchmaker for Microbiomes – Identifying Relationships of Microbes and Metabolites – Scitech Daily

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 23, 2019

In today’s digest read about the Darobactin (a new antibiotic that selectively kills Gram-negative pathogens by binding to the BamA protein, located in the external membrane of Gram-negative bacteria), temporal stability of the rumen microbiota, and Gardnerella species (Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis) in the vaginal microbiome. And, check out 2019 Holiday Gift Guide For Microbe Lovers. Happy weekend!

General microbiome

*A new antibiotic selectively kills Gram-negative pathogens – Yu Imai – Nature

Read the story behind the paper by Roberto Molar Candanosa, Northeastern University.

Gut microbiome

Review: The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health – Jillian L. Waters & Ruth E. Ley – BMC Biology

The gut microbiota influences how circulating immune cells in humans change from one day to the next – Jonas Schluter – bioRxiv

Vaginal microbiome

*Resolution and Cooccurrence Patterns of Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis within the Vaginal Microbiome – Janet E. Hill – Infection and Immunity

Clinical validation of the Aptima Bacterial Vaginosis and Aptima Candida/Trichomonas Vaginitis Assays: results from a prospective multi-center clinical study – Jane R. Schwebke – Journal of Clinical Microbiology

Review: Understanding and interpreting community sequencing measurements of the vaginal microbiome – HL Berman – BJOG : an International Journal of Obstetrics and Gynaecology

Endocervical microbiome

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

Uterine microbiome

Does dysbiotic endometrium affect blastocyst implantation in IVF patients? – Tomoko Hashimoto & Koichi Kyono – Journal of Assisted Reproduction and Genetics

Oral microbiome

Oral microbial community composition is associated with pancreatic cancer: A case‐control study in Iran – Emily Vogtmann – Cancer Medicine

Animal microbiome

*Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements – Timothy J. Snelling – Animal Microbiome

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens – Laura Glendinning – Animal Microbiome

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status – Tucker Andrews – PlosOne

Inulin improves the egg production performance and affects the cecum microbiota of laying hens – Hongmei Shang – International Journal of Biological Macromolecules

Animal experiments

Effects of Debaryomyces hansenii treatment on intestinal mucosa microecology in mice with antibiotic-associated diarrhea – Ao Zeng – PlosOne

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium – Andre Mu – bioRxiv

Hepatitis B Virus Infection Alters Gut Microbiota Composition in Mice – Qingfeng Zhu – Front. Cell. Infect. Microbiol.

Human Gut Microbiome Transplantation in Ileitis Prone Mice: A Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients – Abigail R Basson – Inflammatory Bowel Diseases

Effects of an Escherichia coli exopolysaccharide on human and mouse gut microbiota in vitro – Baiyuan Li – International Journal of Biological Macromolecules

Ion Transport Basis of Diarrhea in a Mouse Model of Adoptive T Cell Transfer Colitis – Dulari Jayawarden – Digestive Diseases and Sciences

Water microbiome

Rewetting of three drained peatlands drives congruent compositional changes in pro- and eukaryotic microbiomes through environmental filtering – Micha Weil – bioRxiv

Phages and viruses

Herpes Simplex Virus Infection, Acyclovir and IVIG Treatment All Independently Cause Gut Dysbiosis – Chandran Ramakrishna – bioRxiv

Svetlana’s pick

Gift guide for this holiday season!
by Justine Dees

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