March 17, 2019

Have a good sunday! Today, we have a quite long digest, containing a variety of articles and studies: reviews about the microbiome and breastfeeding and Parkinson’s disease; microbiota alterations in pulmonary fibrosis, association with stress in pregnant women, and relationships between oral microbiome and pancreatic cancer. And so much more!

 

Human/General Microbiome

Review: Microbiome programming of brain development: implications for neurodevelopmental disorders – Hans Forssberg – Developmental Medicine and Child Neurology

Review: Microbiome, Parkinson’s Disease and Molecular Mimicry – Fabiana Miraglia – Cells

Review: The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut – Janneke Elzinga – Microbiology and Molecular Biology Reviews

Review: Indoles: metabolites produced by intestinal bacteria capable of controlling liver disease manifestation – T. Hendrikx – Journal of Internal Medicine

Review: Shaping the Gut Microbiota by Breastfeeding: The Gateway to Allergy Prevention? – Lieke W. J. van den Elsen – Frontiers in Pediatrics

Minireview: Nonalcoholic fatty liver disease and the gut microbiome: Are bacteria responsible for fatty liver? – Tien S Dong – Experimental Biology and Medicine

Perspectives: Is the fountain of youth in the gut microbiome?John F. Cryan – The Journal of Physiology

Bugs to debug? The exploration of gut microbiome in human health and diseases – Yen-Hsuan Ni – Journal of the Formosan Medical Association

Impact of a bathing tradition on shared gut microbe among Japanese families – Toshitaka Odamaki – Scientific Reports

Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome – Promi Das – BMC Genomics

Fecal and blood microbiota profiles and presence of nonalcoholic fatty liver disease in obese versus lean subjects – Yeojun Yun – PLoS One

H. pylori eradication with antibiotic treatment causes changes in glucose homeostasis related to modifications in the gut microbiota – Gracia Mª Martín-Núñez – PLoS One

Oral microbial dysbiosis in patients with Kostmann syndrome – Nursen Topcuoglu – Journal of Medical Microbiology

Alterations in the gut microbiota of patients with silica-induced pulmonary fibrosis – Yao Zhou – Journal of Occupational Medicine and Toxicology

Association between Psychosocial Stress and Fecal Microbiota in Pregnant Women – C. Hechler – Scientific Reports

Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients – Fu‑Gang Wang – Experimental and Therapeutic Medicine

Role of Fecal Microbiota Transplantation for Maintenance of Remission in Patients with Ulcerative Colitis: A Pilot Study – Ajit Sood – Journal of Crohn’s and Colitis

Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women – Liying Yang – Emerging Microbes & Infections

Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans – Anna M. Seekatz – mSphere

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression – Florian R. Kirchner – Frontiers in Immunology

Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer – Rogier Aäron Gaiser – Gut

Disordered intestinal microbes are associated with the activity of Systemic Lupus Erythematosus – Yao Li – Clinical Science

Long-Term Azithromycin Reduces Haemophilus influenzae and Increases Antibiotic Resistance in Severe Asthma – Steven L Taylor – American Journal of Respiratory and Critical Care Medicine

Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon – Shawn Gurwara – Nutrients

Analysis of the Effects of Dietary Pattern on the Oral Microbiome of Elite Endurance Athletes – Nida Murtaza – Nutrients

 

Animal Microbiome / Animal Experiments

TLR4 May Be Involved in the Regulation of Colonic Mucosal Microbiota by Vitamin A – Lu Xiao – Frontiers in Microbiology

Tunicate-associated bacteria show a great potential for the discovery of antimicrobial compounds – Diah Ayuningrum – PLoS One

Effects of Arsenic on Gut Microbiota and Its Biotransformation Genes in Earthworm Metaphire sieboldi – Hong-Tao Wang – Environmental Science and Technology

A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract – Saad Al-Masaudi – International Microbiology

Species identity dominates over environment in shaping the microbiota of small mammals – S. C. L. Knowles – Ecology Letters

Three types of gut bacteria collaborating to improve Kui Jie’an enema treat DSS-induced colitis in mice – Wei Yu – Biomedicine & Pharmacotherapy

The Skin Commensal Yeast Malassezia Triggers a Type 17 Response that Coordinates Anti-fungal Immunity and Exacerbates Skin Inflammation – Florian Sparber – Cell Host Microbe

Dietary inulin alleviates diverse stages of type 2 diabetes mellitus via anti-inflammation and modulating gut microbiota in db/db mice – Ke Li – Food & Function

Apple consumption is associated with a distinctive microbiota, proteomics and metabolomics profile in the gut of Dawley Sprague rats fed a high-fat diet – Jose F. Garcia-Mazcorro – PLoS One

Sema3A – mediated modulation of NR1D1 expression may be involved in the regulation of axonal guidance signaling by the microbiota – Xunzhong Qia – Life Sciences

Multi-hit early life adversity affects gut microbiota, brain and behavior in a sex-dependent manner – Marion Rincel – Brain, Behavior, and Immunity

Letrozole treatment of adult female mice results in a similar reproductive phenotype but distinct changes in metabolism and the gut microbiome compared to pubertal mice – Pedro J. Torres – BMC Microbiology

Supplementation of dietary non-digestible oligosaccharides from birth onwards improve social and reduce anxiety-like behaviour in male BALB/c mice – Kirsten Szklany – Nutritional Neuroscience

Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract – Dongyao Li – International Journal of Molecular Sciences

Alteration of GLP-1/GPR43 expression and gastrointestinal motility in dysbiotic mice treated with vancomycin – Xin Xu – Scientific Reports

Subchronic low-dose 2,4-D exposure changed plasma acylcarnitine levels and induced gut microbiome perturbations in mice – Pengcheng Tu – Scientific Reports

The influence of the host microbiome on 3,4-methylenedioxymethamphetamine (MDMA)-induced hyperthermia and vice versa – Emily A. Ridge – Scientific Reports

Effects of Dietary Supplementation With Enterococcus faecium and Clostridium butyricum, Either Alone or in Combination, on Growth and Fecal Microbiota Composition of Post-weaning Pigs at a Commercial Farm – Yoshiaki Sato – Frontiers in Veterinary Science

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle – Bing Wang – Frontiers in Microbiology

Intestinal dysbiosis augments liver disease progression via NLRP3 in a murine model of primary sclerosing cholangitis – Lijun Liao – Gut

 

Plant Microbiome

Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight (Phytophthora capsici) – Huixiu Li – Frontiers in Microbiology

 

Other Microbes

Preview: Strain-Level Diversity in the Gut: The P. copri Case  – Amira Metwaly – Cell Host Microbe

 

Bioinformatics and ‘-Omics’

Novel insights from uncultivated genomes of the global human gut microbiome – Stephen Nayfach – Nature

Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing – Jyun-Hong Lin – Journal of Clinical Medicine

Detection of critical antibiotic resistance genes through routine microbiome surveillance – Zachary M. Burcham – PLoS One

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations – Aleksandra I. Perz – BMC Bioinformatics

Rarity of microbial species: In search of reliable associations – Arnaud Cougoul – PLoS One

Stoplight: De novo Assembly Vastly Expands the Known Microbial Universe – Samuel S. Minot – Trends in Microbiology

 

Beneficial Microbes and Compounds

Guarana supplementation attenuated obesity, insulin resistance, and adipokines dysregulation induced by a standardized human Western diet via brown adipose tissue activation Rafael Calixto Bortolin – Phytotherapy Research

Prebiotic supplementation in frail older people affects specific gut microbiota taxa but not global diversity – Tam T. T. Tran – Microbiome

 

Water Microbiome

Composition and Dynamics of the Activated Sludge Microbiome during Seasonal Nitrification Failure – Juliet Johnston – Scientific Reports

 

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March 14, 2019

Today’s digest covers interesting reviews on microbiota for immunotherapies, non-digestible carbohydrates for infant microbiota and contribution of marine microbiota in reactive oxygen species; research articles on how gluten sensitivity is affected by duodenal microbiota and how ginger intake affects mouse microbiota.

General microbiome

Review: Mining the microbiota for microbial and metabolite-based immunotherapies – Ashwin N. Skelly – Nature Reviews Immunology

Pregnancy and early life microbiome

Relationship between vitamin D status and the vaginal microbiome during pregnancy – Kimberly K. Jefferson – Journal of Perinatology

Review: Shaping the Infant Microbiome With Non-Digestible Carbohydrates – Stella A. Verkhnyatskaya – Frontiers in Microbiology

Variations in early gut microbiome are associated with childhood eczema – Yu Zhang – FEMS Microbiology Letters

Human gut microbiome

Gut microbiota in HIV–pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction – Meera K. Shenoy – Microbiome

Effects of bowel preparation on the human gut microbiome and metabolome – Naoyoshi Nagata – Scientific Reports

Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic – Sarah Tomkovich – The Journal of Clinical Investigation

Animal experiments

Host NLRP6 exacerbates graft-versus-host disease independent of gut microbial composition – Tomomi Toubai – Nature Microbiology

Duodenal bacterial proteolytic activity determines sensitivity to dietary antigen through protease-activated receptor-2 – Alberto Caminero – Nature Communications

The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline – Mahdi Ghanbari – Scientific Reports

Beneficial effects of ginger on prevention of obesity through modulation of gut microbiota in mice – Jing Wang – European Journal of Nutrition

Six‐Week High‐Fat Diet Alters the Gut Microbiome and Promotes Cecal Inflammation, Endotoxin Production, and Simple Steatosis without Obesity in Male Rats – Melisa Crawford – Lipids

Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders – Elisabetta Mondo – BioRxiv

The gut microbiota regulates mouse biliary regenerative responses – Wenli Liu – BioRxiv

Plant, root, soil microbiome

Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems – Maria J. Mosqueira – Scientific Reports

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments – Adam J. Kessler – Nature Microbiology

Effects of graphene oxide and graphite on soil bacterial and fungal diversity – Christian Forstner – BioRxiv

Water microbiome and extremophiles

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Non-microbiology picks

Nano-bot can probe inside human cells – Science Daily

March 4, 2019

Human Microbiome

Polyamines and microbiota in bicuspid and tricuspid aortic valve aortopathy – Amalia Forte – Journal of Molecular and Cellular Cardiology

Targeting the Gut Microbiota to Investigate the Mechanism of Lactulose in Negating the Effects of a High-Salt Diet on Hypertension – Zheng Zhang – Molecular Nutrition and Food Research

Food allergy: could the gut microbiota hold the key? – Supinda Bunyavanich – Nature Reviews Gastroenterology & Hepatology

The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases – Mathias L. Richard – Nature Reviews Gastroenterology & Hepatology

Type VI Secretion Systems and the Gut Microbiota –  Michael J. Coyne – Microbiology Spectrum

Autism Spectrum Disorders and the Gut Microbiota – Antonella Fattorusso – Nutrients

New Approaches to Detect Biosynthetic Gene Clusters in the Environment – Ray Chen – Medicines

Impact of microbiota on central nervous system and neurological diseases: the gut-brain axis – Qianquan Ma – Journal of Neuroinflammation

Dysregulated Lung Commensal Bacteria Drive Interleukin-17B Production to Promote Pulmonary Fibrosis through Their Outer Membrane Vesicles – Daping Yang – Immunity

Altered gut microbiome after bariatric surgery and its association with metabolic benefits: A systematic review – Naomi K. Davies – Surgery for Obesity and Related Diseases

Trimethylamine N-oxide, Mediterranean diet, and nutrition in healthy, normal-weight adults: also a matter of sex? – Luigi Barrea – Nutrition

The composition of the pulmonary microbiota in sarcoidosis – an observational study – André Becker – Respiratory Research

Emerging trends and research foci in gastrointestinal microbiome – Xiaoquan Huang – Journal of Translational Medicine

Updates on Clostridioides (Clostridium) difficile Infection With Emphasis on Long-Term Care – Eddie Grace –  The Senior Care Pharmacist

 

Animal Microbiome

Host genetics and diet composition interact to modulate gut microbiota and predisposition to metabolic syndrome in spontaneously hypertensive stroke-prone rats – Arashdeep Singh – The FASEB Journal

Comparative effects of n-hexane and methanol extracts of elecampane (Inula helenium L.) rhizome on growth performance, carcass traits, feed digestibility, intestinal antioxidant status and ileal microbiota in broiler chickens – Mirza-Ebrahim Abolfathi – Archives of Animal Nutrition

Comparison of the Gut Microbiota Composition between the Wild and Captive Tibetan Wild Ass (Equus kiang) – Hongmei Gao – Journal of Applied Microbiology

Consumption of drinking water N-Nitrosamines mixture alters gut microbiome and increases the obesity risk in young male rats – Jianqiang Zhu – Environmental Pollution

Modularity and predicted functions of the global sponge-microbiome network – Miguel Lurgi – Nature Communications

Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice – Kara D. McGaughey – Scientific Report

Loading ceftriaxone, vancomycin, and Bifidobacteria bifidum TMC3115 to neonatal mice could differently and consequently affect intestinal microbiota and immunity in adulthood – RuYue Cheng – Scientific Report

Dietary Protein Intake Level Modulates Mucosal Healing and Mucosa-Adherent Microbiota in Mouse Model of Colitis – Sandra Vidal-Lletjós – Nutrients

Farm stage, bird age and body site dominantly affect the quantity, taxonomic composition, and dynamics of respiratory and gut microbiota of commercial layer chickens – John M. Ngunjiri – Applied and Environmental Microbiology

Development and Function of the Intestinal Microbiome and Potential Implications for Pig Production – Tanya L. Nowland – Animals

Green Coffee Extract Improves Cardiometabolic Parameters and Modulates Gut Microbiota in High-Fat-Diet-Fed ApoE-/- Mice – Erika Caro-Gómez – Nutrients

Dysbiosis of the Gut Microbiota on the Inflammatory Background due to Lack of Suppressor of Cytokine Signalling-1 in Mice – Y. Gendo – Inflammatory Intestinal Diseases

 

Beneficial Microbes and Compounds

Prebiotic supplementation of in vitro faecal fermentations inhibits proteolysis by gut bacteria and host diet shapes gut bacterial metabolism and response to intervention – Xuedan Wang – Applied and Environmental Microbiology

Probiotics and Colon Cancer – Lorenzo Drago – Microorganisms

The Therapeutic Implications of the Gut Microbiome and Probiotics in Patients with NAFLD – Brandon J. Perumpail – Diseases

Cranberry Polyphenols: Natural Weapons against Dental Caries – Nebu Philip – Dentistry Journal

Dietary Components That May Influence the Disturbed Gut Microbiota in Chronic Kidney Disease – Denise Mafra – Nutrients

Liposomal Irinotecan for Treatment of Colorectal Cancer in a Preclinical Model – Jiao-Ren Huang – Cancers

Effects of acupuncture in treating insomnia due to spleen-stomach disharmony syndrome and its influence on intestinal microbiome: Study protocol for a randomized controlled trial –  Ya-ru Huangfu – Journal of Integrative Medicine

Patient perception and approval of faecal microbiota transplantation (FMT) as an alternative treatment option for obesity – F. Gundling – Obesity Science and Practice

 

Water Microbiome

Bacterial release from pipe biofilm in a full-scale drinking water distribution system – Sandy Chan – npj Biofilms and Microbiomes

 

Plant Microbiome

The tea leaf microbiome shows specific responses to chemical pesticides and biocontrol applications – Tomislav Cernava – Science of The Total Environment

Algae bacteria interactions that balance the planktonic microbiome – Emilio Cirri – New Phytologist

 

Bioinformatics

VERA: agent-based modeling transmission of antibiotic resistance between human pathogens and gut microbiota – Oksana E Glushchenko – Bioinformatics

CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis – Tony J. Lam – The CRISPR Journal

 

Other

Impact of primary carbon sources on microbiome shaping and biotransformation of pharmaceuticals and personal care products – Karen Rossmassler – Biodegradation

GrgA as a potential target of selective antichlamydials – Huirong Zhang – PLoS ONE

Quenching by sodium thiosulfate does not influence 16S rRNA gene sequencing profiles of reclaimed water from three sites in the Mid-Atlantic, United States – Sarah M.Allard – Environmental Research

March 1, 2019

Human Microbiome

The human microbiome in health and disease: hype or hope – Gwen Falony – Acta Clinica Belgica

Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities – Daniel Rodríguez Amor – Life

Influence of Crohn’s disease related polymorphisms in innate immune function on ileal microbiome – Ellen Li – PLoS ONE

Interactions between gut microbiota and non-alcoholic liver disease: the role of microbiota-derived metabolites – Kyongbum Lee – Pharmacological Research

Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection – Benjamin H Mullish – Gut

Fecal microbiota dynamics and its relation with disease course in Crohn’s disease – Gianluca Galazzo – Journal of Crohn’s and Colitis

Associations Between Gut Microbiota and Alzheimer’s Disease: Current Evidences and Future Therapeutic and Diagnostic Perspectives – Liang Shen – Journal of Alzheimer’s Disease

Western diet regulates immune status and the response to LPS-driven sepsis independent of diet-associated microbiome – Brooke A. Napier – PNAS

The Human Fecal Microbiota Metabolizes Foodborne Heterocyclic Aromatic Amines by Reuterin Conjugation and Further Transformations – Falco Beer – Molecular Nutrition and Food Research

Clinical Review on the Utility of Fecal Microbiota Transplantation in Immunocompromised Patients – Hamzah Abu-Sbeih – Current Gastroenterology Reports

Cellular and Molecular Therapeutic Targets in Inflammatory Bowel Disease-Focusing on Intestinal Barrier Function – Ida Schoultz – Cells

Can Gut Microbiota and Lifestyle Help Us in the Handling of Anorexia Nervosa Patients? – Vanessa Mendez-Figueroa – Microorganisms

Impact of the Gastro-Intestinal Bacterial Microbiome on Helicobacter-Associated Diseases – Maxime Pichon – Healthcare

Influence of short-term changes in dietary sulfur on the relative abundances of intestinal sulfate-reducing bacteria – Allison Dostal Webster – Gut Microbes

Fecal microbiota transplantation research output from 2004 to 2017: a bibliometric analysis – Yan Li – PeerJ

Conjunctival microbiome changes associated with fungal keratitis: metagenomic analysis – C. Ge – International Journal of Ophthalmology

Gut Microbiota and Chronic Constipation: A Review and Update – Toshifumi Ohkusa – Frontiers in Medicine

An altered fecal microbiota profile in patients with non-alcoholic fatty liver disease (NAFLD) associated with obesity – E. Nistal – The Spanish Journal of Gastroenterology

Paternal Programming of Liver Function and Lipid Profile Induced by a Paternal Pre-Conceptional Unhealthy Diet: Potential Association with Altered Gut Microbiome Composition – X. Zhang – Kidney and Blood Pressure Research

Tryptophan Metabolism and Related Pathways in Psychoneuroimmunology: The Impact of Nutrition and Lifestyle – J. M. Gostner – Neuropsychobiology

The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa – Jochen Seitz – Frontiers in Endocrinology

Sperm Microbiota and Its Impact on Semen Parameters – David Baud – Frontiers in Microbiology

A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016 – NIH Human Microbiome Portfolio Analysis Team – Microbiome

 

Microbiome and Cancer

Impact of chemotherapy on the association between fear of cancer recurrence and the gut microbiota in breast cancer survivors – Ryo Okubo – Brain, Behavior, and Immunity

Bugs, drugs, and cancer: can the microbiome be a potential therapeutic target for cancer management? – Biying Chen – Drug Discovery Today

 

Early Childhood Microbiome

Crosstalk Between the Microbiome and Gestational Immunity in Autism-Related Disorders – Matt J. Paysour – DNA and Cell Biology

Cohort profile: The LoewenKIDS Study – life-course perspective on infections, the microbiome and the development of the immune system in early childhood – Cornelia Gottschick – International Journal of Epidemiology

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month – Nina Iszatt – Microbiome

 

Animal Microbiome

Convergence, constraint and the potential for mutualism between ants and gut microbes – Elizabeth G. Pringle – Molecular Ecology

Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy – Martin Schwarzer – Frontiers in Immunology

Fto Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice via Alterations in Gut Microbiota – Lijuan Sun – Theranostics

 

Beneficial Bugs, Foods and Compounds

Re-purposing is needed for beneficial bugs, not for the drugs – Hari Ram – International Microbiology

Probiotic mixture of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 attenuates hippocampal apoptosis induced by lipopolysaccharide in rats – Ghazaleh Mohammadi – International Microbiology

The Use of Probiotic Therapy to Modulate the Gut Microbiota and Dendritic Cell Responses in Inflammatory Bowel Diseases – Pablo Alagón Fernández del Campo – Medical Sciences

Dietary fibers as emerging nutritional factors against diabetes: focus on the involvement of gut microbiota – Vemana Gowd – Critical Reviews in Biotechnology

Gut microbiota, a new frontier to understand traditional Chinese medicines – Wuwen Feng – Pharmacological Research

Fructooligosaccharides Ameliorating Cognitive Deficits and Neurodegeneration in APP/PS1 Transgenic Mice through Modulating Gut Microbiota – Jing Sun – Journal of Agricultural and Food Chemistry

Short-chain fatty acid delivery: assessing exogenous administration of the microbiome metabolite acetate in mice – Tyler B. Shubitowski – Physiological Reports

Dietary intake of whole strawberry inhibited colonic inflammation in dextran sulfate sodium-treated mice via restoring immune homeostasis and alleviating gut microbiota dysbiosis – Yanhui Han – Journal of Agricultural and Food Chemistry

Ganoderma lucidum polysaccharide improves rat DSS-induced colitis by altering cecal microbiota and gene expression of colonic epithelial cells – Jinli Xie –  Food & Nutrition Research

In Vitro Infant Faecal Fermentation of Low Viscosity Barley β-Glucan and Its Acid Hydrolyzed Derivatives: Evaluation of Their Potential as Novel Prebiotics – Ka-Lung Lam – Molecules

Role of intestinal microecology in the regulation of energy metabolism by dietary polyphenols and their metabolites – Shaoling Lin – Food & Nutrition Research

Neuroprotection of Fasting Mimicking Diet on MPTP-Induced Parkinson’s Disease Mice via Gut Microbiota and Metabolites – Zhi-Lan Zhou – Neurotherapeutics

Refined versus Extra Virgin Olive Oil High-Fat Diet Impact on Intestinal Microbiota of Mice and Its Relation to Different Physiological Variables – Nieves Martínez – Microorganisms

Engineered and wild-type L. lactis promote anti-inflammatory cytokine signalling in inflammatory bowel disease patient’s mucosa – Saša Simčič – World Journal of Microbiology and Biotechnology

Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro – Olaf Perdijk – Frontiers in Immunology

 

Built Environments

Man-made microbial resistances in built environments – Alexander Mahnert – Nature Communications

House dust microbiome and human health risks – Yifan Shan – International Microbiology

Microbiomes of China’s Space Station During Assembly, Integration, and Test Operations – Ying Zhang – Microbial Ecology

 

Environmental and Plant Microbiome

Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses – Cesar A. Pérez-Fernández – International Microbiology

Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils – Zhi-Bo Zhao – Microbiome

The deep continental subsurface: the dark biosphere – Cristina Escudero – International Microbiology

 

Bioinformatics

Batch effects correction for microbiome data with Dirichlet-multinomial regression – Zhenwei Dai – Bioinformatics

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon – Anna Cuscó – F1000Research

 

Methods

Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis – Xiaoxiao Sun – PeerJ

In Vitro Methods to Study Colon Release: State of the Art and An Outlook on New Strategies for Better In-Vitro Biorelevant Release Media – Marie Wahlgren – Pharmaceutics

 

January 28, 2019

Human and General Microbiome

Book Chapter: Necrotizing Enterocolitis and the Preterm Infant Microbiome. – Jillian R. Baranowski – Part of the Advances in Experimental Medicine and Biology book series

Book Chapter: Shaping Microbiota During the First 1000 Days of Life. – Marta Selma-Royo – Part of the Advances in Experimental Medicine and Biology book series

Book Chapter: Targeting Food Allergy with Probiotics. – Lorella Paparo – Part of the Advances in Experimental Medicine and Biology book series

Review: The relation of the vaginal microbiota to early pregnancy development during In Vitro Fertilization treatment-A meta-analysis. – M. Singer – Journal of Gynecology Obstetrics and Human Reproduction

Review: Neuropeptides in the microbiota-brain axis and feeding behavior in autism spectrum disorder. – Sergueï O.Fetissov – Nutrition (Elsevier)

Review: Gut microbiome and cancer immunotherapy. – Weina Li – Cancer Letters

Review: The Microbiome-Host Interaction as a Potential Driver of Anastomotic Leak. – Victoria M. Gershuni – Current Gastroenterology Reports

Review: The links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD). – Zahra Safari – Cellular and Molecular Life Sciences

Review: The role of chronic kidney disease-associated dysbiosis in cardiovascular disease.  – Mark A Bryniarski – Experimental Biology and Medicine

Review: The Interplay between Immunity and Microbiota at Intestinal Immunological Niche: The Case of Cancer. – Rossella Cianci – International Journal of Molecular Sciences

Spotlight: Ethnicity-Influenced Microbiota: A Future Healthcare Perspective. – Madhusmita Dehingia – Trends in Microbiology

Exploration of microbiota targets for major depressive disorder and mood related traits. – Yu-Chu Ella Chung – Journal of Psychiatric Research

Altered fecal bacterial composition correlates with disease activity in inflammatory bowel disease and the extent of IL8 induction. – Farnaz Heidarian – Current Research in Translational Medicine

Metagenome – Inferred bacterial replication rates in cystic fibrosis airways. – Katarzyna Pienkowska – Journal of Cystic Fibrosis

Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus. – Jay Liu – EBioMedicine

Deep sequencing reveals specific bacterial signatures in the subgingival microbiota of healthy subjects. – Eri Ikeda – Clinical Oral Investigations

Close social relationships correlate with human gut microbiota composition. – Kimberly A. Dill-McFarland – Scientific Reports

The gut microbiota heterogeneity and assembly changes associated with the IBD. – Yang Sun – Scientific Reports

The respiratory microbiota: new insights into pulmonary tuberculosis. – Setegn Eshetie – BMC Infectious Diseases

 

Faecal Transplants

Letter to the Editor: Faecal microbiota transplant for eradication of multidrug-resistant Enterobacteriaceae: a lesson in applying best practice? – Benjamin H. Mullish – Clinical Microbiology and Infection

Clinical characteristic and fecal microbiota responses to probiotic or antidepressant in patients with diarrhea-predominant irritable bowel syndrome with depression comorbidity: a pilot study. – Lu Zhang – Chinese Medical Journal

Multi-session fecal microbiota transplantation using colonoscopy has favorable outcomes for the treatment of steroid-dependent ulcerative colitis. – Young-Seok Cho – Intestinal Research

 

Beneficial Microbes and Compounds

Effect of Probiotic Use on Adverse Events in Adult Patients with Inflammatory Bowel Disease: a Retrospective Cohort Study. – Maria Pina Dore – Probiotics and Antimicrobial Proteins

Identification of the novel role of butyrate as AhR ligand in human intestinal epithelial cells. – Ludovica Marinelli – Scientific Reports

Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b metabolic interaction based on 2′-O-fucosyl-lactose studied in steady-state cultures in a Freter-style chemostat. – Manuela Centanni – Applied and Environmental Microbiology

Oral supplements of combined fructo- and xylo-oligosaccharides during perinatal period significantly offsets acrylamide-induced oxidative impairments and neurotoxicity in rats. – Muralidhara Krishna – Journal Of Physiology And Pharmacology

Impact of Grain Sorghum Polyphenols on Microbiota of Normal Weight and Overweight/Obese Subjects during In Vitro Fecal Fermentation. – Danielle Ashley – Nutrients

Geographical location specific composition of cultured microbiota and Lactobacillus occurrence in human breast milk in China. – Mengfan Ding – Food & Function

 

Animal Microbiome

Review: The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States. – Sarah Moraïs – Trends in Microbiology

Gut microbiota affects development and olfactory behavior in Drosophila melanogaster. – Huili Qiao – Journal of Experimental Biology

Genomic diversity landscape of the honey bee gut microbiota. – Kirsten M. Ellegaard – Nature Communications

Abnormal composition of gut microbiota contributes to delirium-like behaviors after abdominal surgery in mice. – Jie Zhang – Neuroscience and Therapeutics

Functional Interactions between Gut Microbiota Transplantation, Quercetin and High Fat Diet Determine Non-Alcoholic Fatty Liver Disease Development in Germ-Free Mice. – David Porras – Molecular Nutrition and Food Research

Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. – Giulia Alessandri – Environmental Microbiology

 

Environmental Microbiome

Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams. – Silas H.W.Vick – iScience

 

Food Microbiome

Book Chapter: Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health. – Laura Lavefve – Advances in Food and Nutrition Research

 

Methodologies

Review: A crash course in sequencing for a microbiologist. – Aleksandra Kozińska – Journal of Applied Genetics

Review: The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies. – Pavan K. Mantravadi – Antibiotics

Effects of the long-term storage of human fecal microbiota samples collected in RNAlater. – Julien Tap – Scientific Reports

A sensitive GC/MS detection method for analyzing microbial metabolites short chain fatty acids in fecal and serum samples. – Shuming Zhang – Talanta

January 11, 2019

General Microbiome

A great-ape view of the gut microbiome.Nishida AH. Nature Reviews Genetics

Relative reduction of biological and phylogenetic diversity of the oral microbiota of diabetes and pre-diabetes patients. Saeb ATM. Microbial Pathogenesis

Dietary modulation of the microbiome as therapy.Bernard NJ. Nature Reviews Rheumatology

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.Pacheco AR. Nature Communications

Low-moisture food matrices as probiotic carriers. Marcial-Coba MS . FEMS Microbiology Letters

REVIEW: Cross-Domain and Viral Interactions in the Microbiome.Rowan-Nash AD. Microbiology and Molecular Biology Reviews

The respiratory microbiome and susceptibility to influenza virus infection. Lee KH. PLoS One

Food Microbiome

Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.Marino M. Food Microbiology

Gut Microbiome

Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway.Singh R. Nature Communications

Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms.Sanctuary MR. PLoS One

Nonsteroidal Anti-inflammatory Drugs Alter the Microbiota and Exacerbate <i>Clostridium difficile</i> Colitis while Dysregulating the Inflammatory Response.Maseda D. mBio

Techniques/Resources

OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes. Yadav D. DNA Research

Streamlining standard bacteriophage methods for higher throughput.Kauffman KM. MethodsX

Indirect DNA extraction method suitable for acidic soil with high clay content. Högfors-Rönnholm E. MethodsX

DATABASE: The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection.Rigden DJ. Nucleic Acid Research

Animal Experiments and Microbiome

Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development.Treichel NS. Microbial Ecology

Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis.Miranda-CasoLuengo R. PLoS One.

Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica.Ramírez-Fernández L. PLoS One

Use of 16S rRNA gene sequencing for prediction of new opportunistic pathogens in chicken ileal and cecal microbiota.Kollarcikova M. Poultry Science

Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.Delgado B. Scientific  Reports

 

Marine and Inland Waters

Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.de Sousa AGG. Microbial Ecology

Stratification, nitrogen fixation, and cyanobacterial bloom stage regulate the planktonic food web structure.Loick-Wilde N. Global Change Biology

Analysis of viral and bacterial communities in groundwater associated with contaminated land.Costeira R. Science of the Total Environment

Plant, Soil, and Air Microbiome

The known and the unknown in soil microbial ecology. Baldrian P. FEMS Microbiology Ecology.

Genomic analysis of bacteria in the Acute Oak Decline pathobiome.Doonan J. Microbial Genomics.

Glutathione S-Transferase Enzymes in Plant-Pathogen Interactions.Gullner G. Frontiers in Plant Science

A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.  Cota-Ruiz K. Environmental International

Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California. Ottesen A. Food Microbiology

Temporal Dynamics of Bacterial Communities in Soil and Leachate Water After Swine Manure Application.Rieke EL. Frontiers of Microbiology

December 16, 2018

A Happy Weekend to one and all. 

Today’s Microbiome Digest features the recent articles covering the techniques and treatments, microbiome of infants, gut, oral, eye and vaginal microbiome, host-microbe interactions, diet and probiotic supplementations, co-culture models and its impact on biofilm reduction, soil microbiome and microbial ecology, comparative study of microbiome in various diseases, role of microbiome on various cancers, metabolomics, animal and insect microbiome, myco and yeast biome, genes and genomics of good and bad bacteria.  ENJOY READING.

TECHNIQUES:

Rapid Determination of Antibiotic Susceptibility by Stimulated Raman Scattering Imaging of D2O Metabolism – Weili Hong – bioRxiv

CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR – Matthew G Links – bioRxiv

Characterization of Hydrocarbon-Degrading Bacteria in Constructed Wetland Microcosms Used to Treat Crude Oil Polluted Water– Amer Jamal Hashmat- Bulletin of Environmental Contamination and Toxicology

A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome – Whidbey C – J Am Chem Soc.

Combined extraction method for metabolomic and PLFA analysis of soil – Jeffrey S.Buyer – Applied Soil Ecology

CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes – Andres Benavides – BMC Genomics

Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli – Yong JunGoh – Current Opinion in Biotechnology

Evaluating the Efficiency of Primer Extension Capture as a Method to Enrich DNA Extractions – Winters M – J Forensic Sci

TREATMENTS:

Intestinal Anti-Inflammatory Activity of the Aqueous Extract from Ipomoea asarifolia in DNBS-Induced Colitis in Rats – da Silva VC – Int J Mol Sci.

Effect of Marine Microalga Chlorella pyrenoidosa Ethanol Extract on Lipid Metabolism and Gut Microbiota Composition in High-Fat Diet-Fed Rats – Wan X – Mar Drugs

Flavonoids and Colorectal Cancer Prevention – Li Y – Antioxidants (Basel)

Effects of Rich-Polyphenols Extract of Dendrobium loddigesii on Anti-Diabetic, Anti-Inflammatory, Anti-Oxidant, and Gut Microbiota Modulation in db/db Mice – Li XW – Molecules

Evidence-based mixture containing Lactobacillus strains and lactoferrin to prevent recurrent bacterial vaginosis: a double blind, placebo controlled, randomised clinical trial – R. Russo – Beneficial Microbes

ORAL MICROBIOME:

Bacterial profile of the supragingival dental biofilm in children with deciduous and early mixed dentition using next generation sequencing (HOMINGS) technique – Harris-Ricardo J – Enferm Infecc Microbiol Clin.

Oral Dysbiosis in Pancreatic Cancer and Liver Cirrhosis: A Review of the Literature – Mohammed H – Biomedicines

Subgingival lipid A profile and endotoxin activity in periodontal health and disease – Strachan A – Clin Oral Investig

GENOME AND GENOMICS:
Iron-associated protein interaction networks reveal the key functional modules related to survival and virulence of Pasteurella multocida – Theeraphol Jatuponwiphat – Microbial Pathogenesis

Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis – Reaz Uddin – Microbial pathogenesis

Epilithic Biofilms in Lake Baikal: Screening and Diversity of PKS and NRPS Genes in the Genomes of Heterotrophic Bacteria – Sukhanova E – Pol J Microbiol.

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa – Fitzgerald CB – BMC Genomics

INSECT MICROBIOME:

Metagenomic 16S rRNA gene sequencing survey of Borrelia species in Irish samples of Ixodes ricinus ticks – John S Lambert – bioRxiv

MARINE MICROBIOME:

Uncultured marine cyanophages encode for active NblA, phycobilisome proteolysis adaptor protein – Omer Nadal – bioRxiv

A fundamental difference between macrobiota and microbial eukaryotes: Protistan plankton has a species maximum in the freshwater-marine transition zone of the Baltic Sea – Filker S – Environ Microbiol

ANTIBIOTIC RESISTANCE:

Antibiotic usage promotes the evolution of resistance against gepotidacin, a novel multi-targeting drug – Petra Szili – bioRxiv

Role of Bentonite on the Mobility of Antibiotic Resistance Genes, and Microbial Community in Oxytetracycline and Cadmium Contaminated Soil – Guo H – Front Microbiol

HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance – Duval M – Proc Natl Acad Sci U S A.

Antibiotics may increase triazine herbicide exposure risk via disturbing gut microbiota – Zhan J – Microbiome

SOIL MICROBIOME:

REVIEW: The rhizosphere microbiome: A key component of sustainable cork oak forests in trouble – Fatima Zahra Maghnia – Forest Ecology and Management

VIROME:

The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics – Diane A.Lima – Virus Research

MYCO and YEAST-BIOME:

Snf2 controls pulcherriminic acid biosynthesis and connects pigmentation and antifungal activity of the yeast Metschnikowia pulcherrima – Deborah Gore-Lloyd – bioRxiv

Nitrogen deprivation in Fusarium oxysporum promotes mycotoxin production via intermediates in the Krebs cycle and unreported methylmalonyl-CoA mutase activity – A. V. Karpe – Metabolomics

METABOLOMICS:

Gut microbiome structure and metabolic activity in inflammatory bowel disease – Eric A. Franzosa – Nature Microbiology

Active Acupoints Differ from Inactive Acupoints in Modulating Key Plasmatic Metabolites of Hypertension: A Targeted Metabolomics Study – Yang M – Sci Rep

Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic – Liu CW – J Proteome Res.

GENERAL MICROBIOME:

The Human Microbiome in Health and Disease – Wyatt M. Arnold – Genomic Applications in Pathology

Microbes: possible link between modern lifestyle transition and the rise of metabolic syndrome – Moossavi S – Obes Rev.

CANCER and MICROBIOTA:

Microbiota in cancer development and treatment – Muhammad Hassan Raza – Journal of Cancer Research and Clinical Oncology

Alcohol and gastrointestinal cancers – Vanella G – Curr Opin Gastroenterol.

Gut microbiota in patients after surgical treatment for colorectal cancer – Jin Y – Environ Microbiol

The Microbiome in Bipolar Depression: A Longitudinal Study of One Pair of Monozygotic Twins – Jiang HY – Bipolar Disord.

Gut Microbiota, Fusobacteria, and Colorectal Cancer – Kelly D – Diseases

PRENATAL AND INFANT MICROBIOME:

The Prenatal Microbiome: A New Player for Human Health – D’Argenio V – High Throughput

Enteric dysbiosis and fecal calprotectin expression in premature infants – Thao T. B. Ho – Pediatric Research

Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in human gut. – Oki K – BMC Microbiol.

EYE MICROBIOME:

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye – Jayasudha R – J Biosci.

GUT MICROBIOME:

Gut microbiota dysbiosis in male patients with chronic traumatic complete spinal cord injury – Zhang C – J Transl Med.

Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome – Treangen TJ – Front Immunol.

A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist – Forbes JD – Microbiome.

Microbiome-The Missing Link in the Gut-Brain Axis: Focus on Its Role in Gastrointestinal and Mental Health – Skonieczna-Żydecka K – J Clin Med.

ANIMAL MICROBIOME:

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

Effects of smoking on the lower respiratory tract microbiome in mice – Zhang R – Respir Res

Evaluating the profound effect of gut microbiome on host appetite in pigs – Yang H – BMC Microbiol.

Comparative analysis of the intestinal bacterial community and expression of gut immunity genes in the Chinese Mitten Crab (Eriocheir sinensis) – Dong J – AMB Express.

Rumen methanogen and protozoal communities of Tibetan sheep and Gansu Alpine Finewool sheep grazing on the Qinghai-Tibetan Plateau, China – Huang J – BMC Microbiol.

PSXIV-15 The Effect Of Intravaginal Progesterone Implant In The Vaginal Microbiota Of Holstein Cows – E Zanella – Journal of Animal Science

The role of the bovine respiratory microbiota in health and disease – T Alexander – Journal of Animal Science

MICROBIAL ECOLOGY:

Polychaete mucopolysaccharide alters sediment microbial diversity and stimulates ammonia-oxidising functional groups – Dale H – FEMS Microbiol Ecol.

Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding – Morales-Cruz A – BMC Microbiol.

The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems – Zhang G – Microbiome

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages – Jacquiod S – Microbiome

Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation – Dai D – Front Microbiol

HOST-MICROBE CROSSTALK:

Neutrophils Restrict Tumor-Associated Microbiota to Reduce Growth and Invasion of Colon Tumors in Mice – Triner D – Gastroenterology

Impact of CFTR modulation with Ivacaftor on Gut Microbiota and Intestinal Inflammation– Ooi CY – Sci Rep

Using Enteric Pathogens to Probe the Gut Microbiota – Spiga L – Trends Microbiol.

DIET, NUTRITION AND PROBIOTICS:

Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition – Svolos V – Gastroenterology

The Dietary Intervention of Transgenic Low-Gliadin Wheat Bread in Patients with Non-Celiac Gluten Sensitivity (NCGS) Showed No Differences with Gluten Free Diet (GFD) but Provides Better Gut Microbiota Profile – Haro C – Nutrients.

SIRT3 Deficiency Promotes High-Fat Diet-Induced Non-Alcoholic Fatty Liver Disease In Correlation With Impaired Intestinal Permeability Through Gut Microbial Dysbiosis – Chen M – Mol Nutr Food Res

Maternal probiotic supplementation for prevention of morbidity and mortality in preterm infants – Grev J – Cochrane Database Syst Rev

Role of prebiotics and probiotics in the functionality of the microbiota in the patients receiving enteral nutrition – Ballesteros Pomar – Nutr Hosp.

Probiotics Streptococcus salivarius 24SMB and Streptococcus oralis 89a interfere with biofilm formation of pathogens of the upper respiratory tract – Bidossi A – BMC Infect Dis

VAGINAL MICROBIOME:

Vaginal dysbiosis, and the risk of human papillomavirus and cervical cancer: systematic review and meta-analysis – Brusselaers N – Am J Obstet Gynecol.

Microbiota dysbiosis is associated with HPV-induced cervical carcinogenesis – Kwasniewski W – Oncol Lett.

CO-CULTURE MODEL and EFFECTS:

Dynamics of Biofilm Formation by Salmonella Typhimurium and Beef Processing Plant Bacteria in Mono- and Dual-Species Cultures – Visvalingam J – Microb Ecol

Anaerobic Degradation of the Plant Sugar Sulfoquinovose Concomitant With H2S Production: Escherichia coli K-12 and Desulfovibrio sp. Strain DF1 as Co-culture Model – Burrichter A – Front Microbiol.