Category Archives: Metabolomics

September 24, 2018

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General microbiology

Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine – Jason Merritt, PHYSICAL REVIEW LETTERS

Small at Size, Big at Impact: Microorganisms for Sustainable Development – Nasib Singh, Microbial Bioprospecting for Sustainable Development

Population Genomics of Archaea: Signatures of Archaeal Biology from Natural Populations – David J. Krause, Population Genomics

Pregnancy and early life

Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum – Aina Gotoh, Scientific Reports

Multi-site human microbiome

Gut–Liver Axis: How Do Gut Bacteria Influence the Liver? – Peter Christopher Konturek, Medical Sciences

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer, Plos One

Optimal immunosuppressor induces stable gut microbiota after liver transplantation – Jian-Wen Jiang, World Journal of Gastroenterology

Human respiratory microbiome

The Microbiome and Tuberculosis: Early Evidence for Cross Talk – Sivaranjani Namasivayam, mBio

Trans-maternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T-cells – Andreas Kyburz, Journal of Allergy and Clinical Immunology

Human oral microbiome

Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situbiofilm model – Stefan Rupf, Scientific Reports

Human gut microbiome

In silico Identification of Metagenomic Signature Describing Neurometabolic Potential of Normal Human Gut Microbiota – A. S. Kovtun, Russian Journal of Genetics

Gut microbiota modulates drug pharmacokinetics – Juanhong Zhang, Drug Metabolism Reviews

Active Site Flexibility Revealed in Crystal Structures of Parabacteroides merdae β‐Glucuronidase from the Human Gut Microbiome – Michael S. Little, Protein Science

Structural and Functional Analysis of the Gut Microbiome for Toxicologists – Robert G. Nichols, Current Protocols in Toxicology

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet, Neurogastroenterology and Motility

Animal experiments

Response of goose intestinal microflora to the source and level of dietary fiber – Haizhu Zhou, Poultry Science

Microbiota modulation by eating patterns, dietary and macronutrient composition; impact on food intake – Elizabeth A. Klingbeil, American Journal of Physiology

Water and extremophile microbiome

Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking – Moa Hägglund, Frontiers in Microbiology

Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N – Beatriz Fernández-Gómez, ISME

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean – Francisco Martinez-Hernandez, ISME

Microbial Community Function in Electroactive Biofilm-based Constructed Wetlands – Ramírez Vargas, Biogeosciences

Fungal endophyte‐infected leaf litter alters in‐stream microbial communities and negatively influences aquatic fungal sporulation – Emily R. Wolfe, Synthesising Ecology

Salt marsh denitrification is impacted by oiling intensity six years after the Deepwater Horizon oil spill – Corianne Tatariw, Environmental Pollution

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination – Blaise P. Bougnom, Environmental Research

Plant, root, and soil microbiome

Phosphate solubilizing bacteria with glucose dehydrogenase gene for phosphorus uptake and beneficial effects on wheat – Muhammad Suleman, Plos One

Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests – Pengyu Zhao, PeerJ

Aphid Colonization Affects Potato Root Exudate Composition and the Hatching of a Soil Borne Pathogen – Grace A. Hoysted, Frontiers in Plant Sciences

Root inoculation with Azotobacter chroococcum 76A enhances tomato plants adaptation to salt stress under low N conditions – Michael James Van Oosten, BMC Plant Biology

Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France) – Jorge R. Osman, Antonie van Leeuwenhoek

Plant roots alter microbial functional genes supporting root litter decomposition – Shengjing Shi, Soil Biology and Biochemistry

Bacterial community response to a preindustrial‐to‐future CO2 gradient is limited and soil‐specific in Texas Prairie grassland – Swastika Raut, Global Change Biology

Built environment

Houseplants as home health monitors – C. Neal Stewart Jr., SYNTHETIC BIOLOGY

Characterization of Aspergillus niger Isolated from the International Space Station – Jillian Romsdahl, mSystems

Food microbiology

Microbiological Changes during Ripening of Chihuahua Cheese Manufactured with Raw Milk and Its Seasonal Variations – Cristina Sánchez-Gamboa, Foods

Supplementation in mushroom crops and its impact on yield and quality – Jaime Carrasco, AMB Express

Aronia (Aronia melanocarpa) Polyphenols Modulate Microbial Community in Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) and Decrease Secretion of Pro‐Inflammatory Markers in a Caco‐2/endothelial Cell Co‐Culture Model – Ting Wu, Molecular Nutrition and Food Research

Techniques

A critical evaluation of the use of gas chromatography- and high performance liquid chromatography-mass spectrometry techniques for the analysis of microbial metabolites in human urine after consumption of orange juice – José Luis Ordóñez, Journal of Chromatography A

Recovering cellular biomass from fluids using chemical flocculation – Paul A. Kenward, Environmental Microbiology Reports

Influence of support media supplementation to reduce the inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier, Data in Brief

A resourceful methodology to profile indolic auxins produced by rhizo-fungi using spectrophotometry and HPTLC – Dhavalkumar Patel, Biotech

Bioinformatics

Computational Tools and Databases of Microbes and Its Bioprospecting for Sustainable Development – Dipannita Hazra, Microbial Bioprospecting for Sustainable Development

Metabolomics

Paradoxes in leaky microbial trade – Yoav Kallus, Nature Communications

Antibiotics

Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen – Gleb Pishchany, PNAS

Microbes in the news

Subculture show converts Storefront for Art and Architecture into living lab – The Architects Newspaper, Ali Oriaku

September 18, 2018

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Quite a few articles of interest today:

  1. Foods that are protective of the gut microbiome: Specific oligosaccharides in breast milk can compensate for the effects of C-section births, and cranberries can compensate for the effects of dietary changes in mice.
  2. A possible bi-directional relationship between the gut microbiome and high altitudes: Specific differences in the gut microbiome are associated with differences in tolerance to high altitudes in males, and exposure to high altitudes can alter the gut microbiome in mice.
  3. Microbes in Space: Nitrogen cycle nicroorganisms that may be able to produce food, water and O2 in space, and exposing desert extremophiles to Martian conditions to learn about the kinds of bacteria on other planets

Also: How smoking impacts the lung virome, the association between fecal microbiome profile and phylogeny in deer genera, and the development of the dust microbiome over time in a classroom

Pregnancy and early life

*Fucosylated oligosaccharides in mother’s milk alleviate the effects of caesarean birth on infant gut microbiota – Katri Korpela – Scientific Reports

The influence of maternal vaginal flora on the intestinal colonization in newborns and 3-month-old infants – Iwona Gabriel – The Journal of Maternal-Fetal & Neonatal Medicine

Fecal Volatile Organic Compounds in Preterm Infants Are Influenced by Enteral Feeding Composition – Sofia el Manouni el Hassani – Sensors

Multi-site human microbiome

Review: Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Human respiratory microbiome

*Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome – Ann C. Gregory – Respiratory Research

Human anal microbiome

Anal microbial patterns and oncogenic HPV in a pilot study of Nigerian men who have sex with men at risk for or living with HIV – Rebecca G Nowak – AIDS Research and Human Retroviruses

Human gut microbiome

*Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – American Journal of Physiology

Intestinal barrier integrity in patients with plaque psoriasis – Mariusz Sikora – The Journal of Dermatology

Review: Mechanisms by which gut microorganisms influence food sensitivities
– Alberto Caminero – Nature Reviews Gastroenterology & Hepatology

Review: Selective sensitivity of the gut microbiome to iron chelators in polybacterial abdominal sepsis – Kayle Dickson – Medical Hypotheses

Review: ADHD-originating in the gut? The emergence of a new explanatory model – Anna M. Sandgren – Medical Hypotheses

Review: Guideline for the Management of Clostridium Difficile Infection in Children and Adolescents With Cancer and Pediatric Hematopoietic Stem-Cell Transplantation Recipients – Caroline Diorio – Journal of Clinical Oncology

Review: Altered Gut Microbiota in Type 2 Diabetes: Just a Coincidence? – Antonio Sircana – Current Diabetes Reports

Review: Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut? – Hanne L.P. Tytgat – Trends in Microbiology

Review: Fecal microbiota transplant – a new frontier in inflammatory bowel disease – Sunkara T – Dove Press

Review: Gut microbiota, cognitive frailty and dementia in older individuals: a systematic review –  Ticinesi A – Dove Press

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Animal experiments

Deletion of poly(ADP‑ribose) polymerase-1 changes the composition of the microbiome in the gut – András Vida – Molecular Medicine Reports

Lactobacillus reuteri F‐9‐35 Prevents DSS‐Induced Colitis by Inhibiting Proinflammatory Gene Expression and Restoring the Gut Microbiota in Mice – Mao‐cheng Sun – Journal of Food Science

*Cranberries attenuate animal-based diet-induced changes in microbiota composition and functionality: A randomized crossover controlled feeding trial – Jose Rodríguez-Morató – The Journal of Nutritional Biochemistry

*The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice – Wei Zhang – PLOS ONE

The Effects of Berberine on the Gut Microbiota in Apc min/+ Mice Fed with a High Fat Diet – Huan Wang – Molecules

The influence of gut microbiota dysbiosis to the efficacy of 5-Fluorouracil treatment on colorectal cancer – Lu Yuan – Biomedicine & Pharmacotherapy

Protein deficiency reduces efficacy of oral attenuated human rotavirus vaccine in a human infant fecal microbiota transplanted gnotobiotic pig model – Ayako Miyazaki – Vaccine

In vitro experiments

Butyrate upregulates the TLR4 expression and the phosphorylation of MAPKs and NK‑κB in colon cancer cell in vitro – Tengfei Xiao – Oncology Letters

Animal microbiome

Comparison of the gut microbiota of captive common bottlenose dolphins, Tursiops truncatus in three aquaria – Akihiko Suzuki – Journal of Applied Microbiology

Bacteria richness and antibiotic-resistance in bats from a protected area in the Atlantic Forest of Southeastern Brazil – Vinícius C. Cláudio – PLOS ONE

*Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae – Jiaying Li – Frontiers in Microbiology

Probiotics modify body weight together with anxiety states via pro-inflammatory factors in HFD-treated Syrian golden hamster – Ennio Avolio – Behavioural Brain Research

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics – Jong Nam Kim – Asian-Australas Journal of Animal Sciences

The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency – Chloe Matthews – Gut

MicrobesEvaluation of conjunctival microbiota in clinically normal persian squirrels (Sciurus Anomalus) – Houman Faghihi – Journal of Zoo and Wildlife Medicine

Plant, root, and soil microbiome

Trichoderma gamsii affected herbivore feeding behaviour on Arabidopsis thaliana by modifying the leaf metabolome and phytohormones – Dongmei Zhou – Microbial Biotechnology

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Soil microbial response to Rhododendron understory removal in southern Appalachian forests: Effects on extracellular enzymes – Ernest D. Osburn – Soil Biology and Biochemistry

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing – Zhiying Li – Current Microbiology

Bacterial diversity in rhizosphere of Paspalum scrobiculatum L. (kodo millet) is revealed with shotgun metagenome sequencing and data analysis – Ratna Prabha – Data in Brief

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Microbial Ecology

Effects of Cd, Cu, Zn and their combined action on microbial biomass and bacterial community structure – Jiuwei Song – Environmental Pollution

Effects of graphene oxides and silver-graphene oxides on aquatic microbial activity – Kwanyoung Ko – Science of The Total Environment

Built environment

*Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten – Anders B. Nygaard – Microbiome

Microbiological analysis of contact lens cases: impact of the hospital environment – Vinicius Targa Villas Bôas – Arquivos Brasileiros de Oftalmologia

Microbes in space

*Nitrogen cycle microorganisms can be reactivated after Space exposure – Ralph E. F. Lindeboom – Scientific Reports

*Desert cyanobacteria under space and planetary simulations: a tool for searching for life beyond Earth and supporting human space exploration – Daniela Billi – International Journal of Astrobiology

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Bioinformatics

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis – Gherman V. Uritskiy – Microbiome

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations  – Alex N Salazar – Bioinformatics

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Microbes in the news

The electrifying energy of gut microbes – Laty A. Cahoon – Nature News and Views

Bacteria and Art

How Anicka Yi’s Science Experiments Are Expanding the Boundaries of Art – Andrew Russeth – W

 

 

September 15, 2018

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Have a nice weekend! Today, we have several papers, covering different aspects of the microbiome! Some highlights (in bold): the role of microbiota in cancer immunotherapy success; interesting study about the lung microbiota and smoking; changes in gut microbiota in asthma patients, microbiota changes in high-salt feces; an interesting article about the potential effect of dogs in veteran rehabilitation; a review about periodontitis and the microbiome; a ecophylogenetic study about mammalian microbiome, and more!

 

Human and General Microbiome

Metagenomic Approaches for Understanding New Concepts in Microbial Science – Luana de Fátima Alves – International Journal of Genomics

Review: Epigenetic Mechanisms Link Maternal Diets and Gut Microbiome to Obesity in the Offspring – Yuanyuan Li – Frontiers in Genetics

Review: NLRP3 inflammasome in colitis and colitis-associated colorectal cancer – Agampodi Promoda Perera – Mammalian Genome

Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study – He Xu – Frontiers in Microbiology

Review: Roles of intestinal microbiota in response to cancer immunotherapy – Jing Cong – European Journal of Clinical Microbiology & Infectious Diseases

Intestinal dysbiosis and hormonal neuroendocrine secretion in the fibromyalgic patient: Relationship and correlations – Giovanni Tomasello – Biomedical Papers

Macroecology to Unite All Life, Large and Small – Ashley Shade – Trends in Ecology and Evolution

Dichotomous development of the gut microbiome in preterm infants – Thao T. B. Ho – Microbiome

Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome – Ann C. Gregory – Respiratory Research

A metagenome-wide association study of gut microbiota in asthma in UK adults – Qi Wang – BMC Microbiology

The Cutaneous Microbiome and Wounds: New Molecular Targets to Promote Wound Healing – Taylor R. Johnson – International Journal of Molecular Sciences

Phthalate Exposure and Odds of Bacterial Vaginosis Among U.S. Reproductive-Aged Women, NHANES 2001-2004 – Ruth J.Geller – Reproductive Toxicology

Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria – Ian J. Passmore – PLoS Pathogens

Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans – E. H. Seck – International Journal of Obesity

The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota – Z.F. Kispal – Journal of Pediatric Urology

The Gut-Brain Axis in Alzheimer’s Disease and Omega-3. A Critical Overview of Clinical Trials – Francesca La Rosa – Nutrients

Associations between Flavonoid Intakes and Gut Microbiota in a Group of Adults with Cystic Fibrosis – Li Li – Nutrients

Review: Insights into the Human Virome Using CRISPR Spacers from Microbiomes – Claudio Hidalgo-Cantabrana – Viruses

Review: Probiotics in the Treatment of Colorectal Cancer –  Robert Hendler – Medicines

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease – Shu Mei Teo – Cell Host and Microbe

Human skin volatiles: Passive sampling and GC × GC-ToFMS analysis as a tool to investigate the skin microbiome and interactions with anthropophilic mosquito disease vectors – Alexis P. Roodt – Journal of Chromatography B

Commentary: Regulating stool for microbiota transplantation – Pilar N. Ossorio – Gut Microbes

Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – Gastrointestinal and Liver Physiology

Exploring service dogs for rehabilitation of veterans with PTSD: A microbiome perspective – Andrew J.,Billera Hoisington – Rehabilitation Psychology

Mucosal associated invariant T cells from human breast ducts mediate a Th17-skewed response to bacterially exposed breast carcinoma cells – Nicholas A. Zumwalde – Breast Cancer Research

Periodontitis and the microbiome: a systematic review and meta-analysis – Fabrizio Guerra – Minerva Stomatologica

Formal Comment: The microbiome and the human: A reply to Parke and colleagues – Tobias Rees – PLoS Biology

Microbiota-gut-brain research: a critical analysis – Katarzyna B. Hooks – Behavioral and Brain Sciences

 

Animal Microbiome

Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota – Christopher A. Gaulke – mBio

The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis – Agnieszka D. Truax – Cell Host and Microbe

American ginseng microbial metabolites attenuate DSS-induced colitis and abdominal pain – Chong-Zhi Wang – International Immunopharmacology

Impact of violacein from Chromobacterium violaceum on the mammalian gut microbiome – Heidi Pauer – PLoS ONE

Bacterial community composition in the salivary glands of triatomines (Hemiptera: Reduviidae) – Michele Souza Lima – PLoS Neglected Tropical Diseases

Postnatal Administration of Lactobacillus rhamnosus HN001 Ameliorates Perinatal Broad-Spectrum Antibiotic-Induced Reduction in Myelopoiesis and T cell Activation in Mouse Pups – Eva Fuglsang – Molecular Nutrition and Food Research

Absorption of Codonopsis pilosula Saponins by Coexisting Polysaccharides Alleviates Gut Microbial Dysbiosis with Dextran Sulfate Sodium-Induced Colitis in Model Mice – Yaping Jing – BioMed Research International

Tributyrin Supplementation Protects Immune Responses and Vasculature and Reduces Oxidative Stress in the Proximal Colon of Mice Exposed to Chronic-Binge Ethanol Feeding – B. Glueck – Journal of Immunology Research

Fecal Hyodeoxycholic Acid Is Correlated With Tylosin-Induced Microbiome Changes in Growing Pigs – Michaela P. Trudeau – Frontiers in Veterinary Science

Yeast Probiotics Shape the Gut Microbiome and Improve the Health of Early-Weaned Piglets – Jinqiang Xu – Frontiers in Microbiology

Probiotic Bacillus amyloliquefaciens C-1 Improves Growth Performance, Stimulates GH/IGF-1, and Regulates the Gut Microbiota of Growth-Retarded Beef Calves – Renjia Du – Frontiers in Microbiology

The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish – Jacquelyn Jones – Frontiers in Microbiology

Intestinal Microbiome-Metabolome Responses to Essential Oils in Piglets – Yuan Li – Frontiers in Microbiology

Review: Managing the Microbial Community of Marine Fish Larvae: A Holistic Perspective for Larviculture – Olav Vadstein – Frontiers in Microbiology

Functional modulation of caecal fermentation and microbiota in rat by feeding bean husk as a dietary fibre supplement – H. Myint – Beneficial Microbes

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics – Jong Nam Kim – Asian-Australian Journal of Animal Sciences

The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice – Wei Zhang – PLoS ONE

 

Food Microbiome

Lactic Acid Bacterium Population Dynamics in Artisan Sourdoughs Over One Year of Daily Propagations Is Mainly Driven by Flour Microbiota and Nutrients – Fabio Minervini – Frontiers in Microbiology

Effect of Pressure, Reconstituted RTE Meat Microbiota, and Antimicrobials on Survival and Post-pressure Growth of Listeria monocytogenes on Ham – Januana S. Teixeira – Frontiers in Microbiology

 

Plant Microbiome

G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla – Mohamed S. Sarhan – Microbes and Environments

Root exudates drive the soil-borne legacy of aboveground pathogen infection – Jun Yuan – Microbiome

Review: Mycorrhizal microbiomes – Mika T. Tarkka – Mycorrhiza

 

Bioinformatics

GePMI: A statistical model for personal intestinal microbiome identification – Zicheng Wang – npj Biofilms and Microbiomes

Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes – Suzanne M. Kosina – BMC Microbiology

 

Other

Temporal variability and stability of the fecal microbiome: the Multiethnic Cohort Study – Benjamin C Fu – Cancer Epidemiology, Biomarkers & Prevention

A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria – Samuel H. Light – Nature

 

September 10, 2018

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In the today’s digest: an article on detection limits and bias with DNA extraction kits and primer choice, a novel R package to analyze timeseries in the 16S microbiome data in perturbation studies, a study on how fecal microbiota transplantation induces changes in gut microbial and metabolomic profiles of pediatric ulcerative colitis patients, plus an invitation for the first worldwide online open access course via Twitter about science and microbiology starting October 2.

Event

Third Annual Microbiome Symposium at Stanford, September 24 at the Stanford Faculty Club, Palo Alto, CA.

Human gut microbiome

*Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients – David J Nusbaum – FEMS Microbiology Ecology

Review: Sample preparation and recent trends in volatolomics for diagnosing gastrointestinal diseases – Tomasz Majchrzak – TrAC Trends in Analytical Chemistry

Special Report: The role of gut microbiota in lupus: what we know in 2018? – Lorena Ruiz – Expert Review of Clinical Immunology

Human gut virome

The Intestinal Virome and Immunity – Jessica A. Neil and Ken Cadwell – J Immunology

Human lung microbiome

The Human Respiratory Microbiome: The End of the Beginning? – Alicia B. Mitchell and Allan R. Glanville – Essentials in Lung Transplantation

Human oral microbiome

Review: The oral microbiome – friend or foe? – Kilian Mogens – Eur J Oral Science

Animal microbiome

Ultrahigh-throughput functional profiling of microbiota communities – Stanislav S. Terekhova – PNAS

Water microbiome

*Investigation of Detection Limits and the Influence of DNA Extraction and Primer Choice on the Observed Microbial Communities in Drinking Water Samples Using 16S rRNA Gene Amplicon Sequencing – Jakob Brandt and Mads Albertsen – Frontiers in Microbiology

Application of untargeted metabolomics for the detection of pathogenic Naegleria fowleri in an operational drinking water distribution system – Zhihao Yu – Water Research

Soil microbiome

Investigation on microbial community in remediation of lead-contaminated soil by Trifolium repensL. – Chenjing Liu – Ecotoxicology and Environmental Safety

Bioinformatics

*The Block Bootstrap Method for Longitudinal Microbiome Data – Pratheepa Jeganathan – arXiv

*Course

#EUROmicroMOOC: Trends in Microbiology [The first worldwide online open access microbiology course via Twitter]

September 1, 2018

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Have a nice weekend! Today, several reviews about different aspects of human genome (from Vitamin D to the Impact of Colonialism in the changes of health in Indigenous people). Today, we have also several studies about poultry microbiome and changes in food microbiota, in addition with interesting studies about microbiota drug metabolism.

 

General and Human Microbiome

Review: The hygiene hypothesis at a glance: early exposures, immune mechanism and novel therapies – Gabriel M.Alexandre-Silva – Acta Tropica

Review: Dietary vitamin D, vitamin D receptor, and microbiome – Jun Sun – Current Opinion in Clinical Nutrition and Metabolic Care

Theory and Synthesis: Consequences of colonialism: A microbial perspective to contemporary Indigenous health – Emily Skelly – American Journal of Physical Anthropology

Review: Early-Life Exposures and Risk of Diabetes Mellitus and Obesity – Véronique Gingras – Current Diabetes Reports

Review: Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer – Veronica Lazar – Frontiers in Immunology

Review: Early Disruption of the Microbiome Leading to Decreased Antioxidant Capacity and Epigenetic Changes: Implications for the Rise in Autism – Rebecca S. Eshraghi – Frontiers in Cellular Neuroscience

Review: Energy balance and gastrointestinal cancer: risk, interventions, outcomes and mechanisms – Cornelia M. Ulrich – Nature Reviews Gastroenterology & Hepatology

Review: Microbial Production of Conjugated Linoleic Acid and Conjugated Linolenic Acid Relies on a Multienzymatic System – Ana S. Salsinha – Microbiology and Molecular Biology Reviews

News & Views: Gut microbiome, microbial metabolites and the development of NAFLD – Cyrielle Caussy – Nature Reviews Gastroenterology & Hepatology

Does Severity of Alzheimer’s Disease Contribute to Its Responsiveness to Modifying Gut Microbiota? A Double Blind Clinical Trial – Azadeh Agahi – Frontiers in Neurology

Evaluation of relationship between dental caries, diabetes mellitus and oral microbiota in diabetics – Bhagyashri Ramachandra Latti – Journal of Oral and Maxillofacial Pathology

Effects of Japanese diet in combination with exercise on visceral fat accumulation – Masaki Asano – Nutrition

Enteric Virome and Bacterial Microbiota in Children with Ulcerative Colitis and Crohn’s Disease – Melissa A. Fernandes – Journal of Pediatric Gastroenterology and Nutrition

Temporal instability of the post-surgical maxillary sinus microbiota – Ioannis Koutsourelakis – BMC Infectious Diseases

Influence of cigarette smoking on the human duodenal mucosa-associated microbiota – Erin R. Shanahan – Microbiome

 

Animal Microbiome

Review: A Review of Prebiotics Against Salmonella in Poultry: Current and Future Potential for Microbiome Research Applications – Andrew C. Micciche – Frontiers in Veterinary Science

Gut Microbiota and Relevant Metabolites Analysis in Alcohol Dependent Mice – Guanhao Wang – Frontiers in Microbiology

Gut microbiota mediates the anti-obesity effect of calorie restriction in mice – Shuo Wang – Scientific Reports

Effect of humic substances on rumen fermentation, nutrient digestibility, methane emissions, and rumen microbiota in beef heifers – Stephanie A Terry – Journal of Animal Science

Effects of glucose oxidase on growth performance, gut function, and cecal microbiota of broiler chickens – Shengru Wu – Poultry Science

16S ribosomal RNA sequencing reveals a modulation of intestinal microbiome and immune response by dietary L-theanine supplementation in broiler chickens – Muhammad Saeed – Poultry Science

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) – Jeremiah J. Minich – Microbiology Open

Effect of oat hulls as a free choice feeding on broiler performance, short chain fatty acids and microflora under a mild necrotic enteritis challenge – Sarbast K.Kheravii – Animal Nutrition

Application of Illumina-MiSeq high throughput sequencing and culture-dependent techniques for the identification of microbiota of silver carp (Hypophthalmichthys molitrix) treated by tea polyphenols – Shiliang Jia – Food Microbiology

 

Beneficial Microbes and Compounds

Rhubarb Peony Decoction Ameliorates Ulcerative Colitis in Mice by Regulating Gut Microbiota to Restoring Th17/Treg Balance – Shuang Luo – Journal of Ethnopharmacology

Bifidobacterium bifidum PRL2010 alleviates intestinal ischemia/reperfusion injury – Sabrina Duranti – PLoS One

Beneficial Effect of Virgin Coconut Oil on Alloxan-Induced Diabetes and Microbiota Composition in Rats – Sinisa Djurasevic – Plant Foods for Human Nutrition

 

Food Microbiome

Microbiota dynamics and volatilome profile during stink bean fermentation (Sataw-Dong) with Lactobacillus plantarum KJ03 as a starter culture – Krittanon Jampaphaeng – Food Microbiology

Microbial spoilage investigation of thawed common cuttlefish (Sepia officinalis) stored at 2 °C using next generation sequencing and volatilome analysis – F. F. Parlapani – Food Microbiology

Exploring core functional microbiota responsible for the production of volatile flavour during the traditional brewing of Wuyi Hong Qu glutinous rice wine – Zi-Rui Huang – Food Microbiology

Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis – Zhongyuan Li – Food Microbiology

Influence of lactate and acetate removal on the microbiota of French fresh pork sausages – Agnès Bouju-Albert – Food Microbiology

 

Plant Microbiome

The future has roots in the past: the ideas and scientists that shaped mycorrhizal research – Paola Bonfante – New Phytology Trust

 

Experiments

Chemoselective Probe Harboring a Unique Bioorthogonal Cleavage Site for Investigation of Gut Microbiota Metabolism – Neeraj Garg – Angewandte Chemie  

An ex vivo fermentation screening platform to study drug metabolism by human gut microbiota – Evita van de Steeg – Drug Metabolism and Disposition

 

August 31, 2018

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Today’s digest features the rumen microbiome from a culturomics point of view, case study of Lactobacillus and Bifidobacterium strains that helped a boy with short bowel syndrome, aging cheese in Murray’s urban caves, and much more. And, check out my non-microbiology pick that can help you become a better writer! Happy September!

Human microbiome

Worldwide Variation in Human Milk Metabolome: Indicators of Breast Physiology and Maternal Lifestyle? – Melvin C. L. Gay – Nutrients

Animal microbiome

*Insights Into Culturomics of the Rumen Microbiome – Tamar Zehavi – Front. Microbiol.

Review: Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present and future – Sharon Ann Huws – Front. Microbiol.

Lactic acid treatment of by-products and phosphorus level in the diet modulate bacterial microbiome and the predicted metagenome functions using the rumen simulation technique – Barbara U.Metzler-Zebeli – Journal of Dairy Science

Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons) – Wenzel Marius – PLoS One

Probiotics

*D-lactic Acidosis: Successful Suppression of D-lactate–Producing Lactobacillus by Probiotics – Bahtiyar Yilmaz – Paediatrics

Cholesterol-lowering effect of Lactobacillus rhamnosus BFE5264 and its influence on the gut microbiome and propionate level in a murine model – Soyoung Park – PLoS One

Effects of lactoferrin on neonatal pathogens and Bifidobacterium breve in human breast milk – Tabitha Woodman – PLoS One

Water microbiome

Nitrifying and Denitrifying Bacterial Communities in Advanced Nitrogen-Removal Onsite Wastewater Treatment Systems – Sara Wigginton – Journal of Environmental Quality – Environmental Microbiology

Soil microbiome

Preprint: Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities – Paul Carini – bioRxiv

Microbes in the news

*The Art and Science of Aging Cheese – Crystal Shi – The Epoch Times

Svetlana’s non-microbiology pick

*A great and neat tips list for all interested in better writing: Five common writing mistakes new scientists make – Jacquelyn Gill

August 25 2018

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Todays Microbiome Digest covers the topics on microbiome of animalia kingdom ranging from humans ⇒mammals ⇒ amphibians ⇒ insects , cyanobacteria, AMR versus AMS, host microbe interactions, how & which microbes create homeostatis in the human body sites.  Happy Reading!

GUT or INTESTINAL MICROBIOME:

Gut microbiome: Microflora association with obesity and obesity-related comorbidities – Lone JB – Microb Pathog

Relevance of gut microbiota in cognition, behaviour and Alzheimer’s disease – de J R De-Paula V – Pharmacol Res.

Small intestinal microbiota: the neglected stepchild needed for fat digestion and absorption – Chang EB – Gut Microbes.

Prospects for Primary Prevention of Type 1 Diabetes by Restoring a Disappearing Microbe – Insel R – Pediatr Diabetes

ANIMAL MICROBIOME:

Synergetic action between the rumen microbiota and bovine health – Zeineldin M – Microb Pathog

Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig and mouse gut microbiomes – Li X – Gigascience

Analyses of Aerosol Concentrations and Bacterial Community Structures for Closed Cage Broiler Houses at Different Broiler Growth Stages in Winter – Jiang L – J Food
Prot.

Characterization of the bacterial community of braised chicken, a specialty poultry product in China – Liu DY – Poult Sci.

Metagenomics analysis reveals significant modulation of cecal microbiota of broilers fed palm kernel expeller diets – Chen WL- Poult Sci.

Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone – Xue D – J Microbiol.

INSECT MICROBIOME:

Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation –
Oliveira JL – PLoS Negl Trop Dis.

FISH MICROBIOME:

Dietary salt levels affect digestibility, intestinal gene expression, and the microbiome, in Nile tilapia (Oreochromis niloticus) – Hallali E – PLoS One

WATER MICROBIAL ECOLOGY:

Bacterial bioclusters relate to hydrochemistry in New Zealand groundwater – Sirisena KA – FEMS Microbiol Ecol

 

PLANT MICROBIOME:

Technique : Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures – Cornet L – Microb Genom

High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil – Bourceret
A – Environ Sci Pollut Res Int.

 

INFANT MICROBIOME:

Investigating the effects of cesarean delivery and antibiotic use in early childhood on risk of later attention deficit hyperactivity disorder – Axelsson PB – J Child
Psychol Psychiatry

 

PROBIOTICS or PREBIOTICS:

The effect of a multispecies probiotic on microbiota composition in a clinical trial of patients with diarrhea-predominant irritable bowel syndrome – Hod K –
Neurogastroenterol Motil.

ANTI- MICROBIAL RESISTANCE and SUSCEPTANCE:

Un-segregated waste disposal: an alarming threat of antimicrobials in surface and ground water sources in Delhi – Velpandian T – Environ Sci Pollut Res Int.

Novel bioactive peptides from PD-L1/2, a type 1 ribosome inactivating protein from Phytolacca dioica L. Evaluation of their antimicrobial properties and anti-biofilm
activities – Pizzo E – Biochim Biophys Acta

 

RESPIRATORY MICROBIOME:

Lower airway microbiota for ‘biomarker’ measurements of cystic fibrosis disease progression – Sherrard LJ – Thorax

Sputum microbiota is predictive of long-term clinical outcomes in young adults with cystic fibrosis – Acosta N- Thorax

 

HOST MICROBE INTERACTIONS:

Preventive effects of bovine colostrum supplementation in TNBS-induced colitis in mice – Filipescu IE – PLoS One

Role of wnt5a in metabolic inflammation in humans – Relling I – J Clin Endocrinol Metab.

 

TECHNIQUES:

Review: Evidence-Based Strategies for the Prehabilitation of the Abdominal Wall Reconstruction Patient – Joslyn NA – Plast Reconstr Surg.

QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling – Zheng B – Sci China Life Sci.

Review: Advances in Imaging Specific Mediators of Inflammatory Bowel Disease – Dmochowska N – Int J Mol Sci.

 

NUTRITION or DIET and TREATMENT:

Glucomannan hydrolysate promotes gut proliferative homeostasis and extends lifespan in Drosophila melanogaster – Si Y – J Gerontol A Biol Sci Med Sci.

Cultivable butyrate-producing bacteria of elderly Japanese diagnosed with Alzheimer’s disease – Nguyen TTT – J Microbiol.

Efficacy of Proanthocyanidins from Pelargonium sidoides Root Extract in Reducing P. gingivalis Viability While Preserving Oral Commensal S. salivarius – Savickiene N –
Materials (Basel).

Effects of Tempeh Fermentation with Lactobacillus plantarum and Rhizopus oligosporus on Streptozotocin-Induced Type II Diabetes Mellitus in Rats – Huang YC – Nutrients

August 18, 2018

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The virome of California mosquitoes, effects of climate warming on grassland microbial communities, and a few “bacteria and art” entries including a 92-foot inflatable E. coli sculpture.

General microbiome

Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction – Stephan Noack – Trends in Biotechnology

Growth tradeoffs produce complex microbial communities on a single limiting resource – Michael Manhart – Nature Communications

Human oral microbiome

Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay – Majda Dzidic – The ISME Journal

Animal experiments

Loss of HDAC6 alters gut microbiota and worsens obesity – Arnon D Lieber – The FASEB Journal

Animal microbiome

Pre-print: CRISPR/Cas9-mediated gene deletion of the ompA gene in an Enterobacter gut symbiont impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes – Shivanand Hegde – bioRxiv

Plant, root, and soil microbiome

Climate warming leads to divergent succession of grassland microbial communities – Xue Guo – Nature Climate Change

Water and extremophile microbiome

Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams – Scott Hotaling – Microbial Ecology

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration – Sylvain Monteux – The ISME Journal

Phages and viruses

Virome of > 12 thousand Culex mosquitoes from throughout California – Mohammadreza Sadeghi – Virology

Comprehensive comparative analysis of methods and software for identifying viral integrations – Xun Chen – Briefings in Bioinformatics

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe – Alfred Fillol-Salom – The ISME Journal

Metabolomics

Metabotypes Related to Meat and Vegetable Intake Reflect Microbial, Lipid and Amino Acid Metabolism in Healthy People – Runmin Wei – Molecular Nutrition & Food Research

More microbes

Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea – Michaeline B N Albright – Microbial Ecology

Bacteria art

Linen and Bacteria: The Hidden History of Microbiology – Clara Rodríguez Fernández – Labiotech.eu

Pomona Arts: Sara Parent Ramos: Jumble, Bunch, Grow – Inland Empire

Oxford Natural History exhibition explores benefits of bacteria – BBC News

August 9, 2018

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Horizontal gene transfer in microbiomes, metabolic study of the microbiota isolated from the camel rumen, a review on the bacteriophage virome in IBD.

General microbiome

Review: Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives – Rafael Pinilla-Redondo – Plasmid

Review: Learning from bacterial competition in the host to develop antimicrobials – Manuela Raffatellu – Nature Medicine

Pregnancy and early life

Early life colonization of the human gut: microbes matter everywhere – Katri Korpela – Current Opinion in Microbiology

Human respiratory microbiome

Determinants of the Nasal Microbiome: Pilot Study of Effects of Intranasal Medication Use – Vijay R Ramakrishnan – Allergy & Rhinology

Human skin microbiome

Sensitive scalp is associated with excessive sebum and perturbed microbiome – Li Ma – Journal of Cosmetic Dermatology

Animal experiments

Effects of host genetics and environmental conditions on fecal microbiota composition of pigs – Tereza Kubasova – PLOS ONE

Animal microbiome

A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation – Javad Gharechahi – Biotechnology for Biofuels

Plant, root, and soil microbiome

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota – Allen Van Deynze – PLOS Biology

Brazilian Ironstone Plant Communities as Reservoirs of Culturable Bacteria With Diverse Biotechnological Potential – Washington L Caneschi – Frontiers in Microbiology

Water and extremophile microbiome

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change – Trine Markussen – Environmental Microbiology

Pre-print: Resource diversity structures aquatic bacterial communities – Mario E Muscarella – bioRxiv

Pre-print: Modular assembly of polysaccharide-degrading microbial communities in the ocean – Tim N Enke – bioRxiv

Food microbiology

Review: Bakery yeasts, a new model for studies in ecology and evolution – Belen Carbonetto – Yeast

Inferences from inventories of microbes in ecological vineyard settings – Hans-Josef Schroers – International Journal of Environmental Quality

Phages and viruses

Review: Bacteriophage virome in IBD – Clemens Thoma – Nature Reviews Gastroenterology and Hepatology

Bioinformatics

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis – Simon A Hardwick – Nature Communications

August 5, 2018

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Have a good sunday! Today, in Microbiome Digest: several reviews focused in clinical aspects of the microbiome, associations between malnutrition and dysbiosis, a study observing the effect of prebiotics on autism spectrum disorders, influence of the microbiome on mouse brain, the impact of storage and DNA extraction on microbiota analysis, and much more!

 

Human and General Microbiome

Review: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human – Anthony P. Corfield – Microorganisms

Review: Next generation microbiology and cystic fibrosis diagnostics: are we there yet? – Claus Moser – Current Opinion in Pulmonary Medicine

Review: Proton Pump Inhibitors: Risks and Rewards and Emerging Consequences to the Gut Microbiome –  Amandeep Singh – Nutrition in Clinical Practice

Review: The Gut Microbiome in Patients with Intestinal Failure: Current Evidence and Implications for Clinical Practice – Esther Neelis – Journal of Parenteral and Enteral Nutrition

Review: The Esophageal Microbiome in Health and Disease – Brooke Corning – Current Gastroenterology Reports

Review: Microbiota issue in CKD: how promising are gut-targeted approaches? – Carmela Cosola – Journal of Nephrology

Review: Neuroimmunophysiology of the gut: advances and emerging concepts focusing on the epithelium – Keith A. Sharkey – Nature Reviews Gastroenterology & Hepatology

Commentary: The Perturbance of Microbiome and Gut-Brain Axis in Autism Spectrum Disorders – Greta Fowlie – International Journal of Molecular Sciences

Comment: Causality in dietary interventions-building a case for gut microbiota – Yan Y. Lam – Genome Medicine

Emergent simplicity in microbial community assembly – Joshua E. Goldford – Science

Contraception: Influence on Vaginal Microbiota and Identification of Vaginal Lactobacilli Using MALDI-TOF MS and 16S rDNA Sequencing – Sonia E. Fosch – The Open Microbiology Journal

Gut Microbiota Dysbiosis is Associated with Malnutrition and Reduced Plasma Amino Acid Levels: Lessons from Genome-Scale Metabolic Modeling – Manish Kumar – Metabolic Engineering

Photobiomodulation of the microbiome: implications for metabolic and inflammatory diseases – Brian Bicknell – Lasers in Medical Science

Roxithromycin regulates intestinal microbiota and alters colonic epithelial gene expression – Cheng Zhang – Applied Microbiology and Biotechnology

Whole Cell Cross-Linking to Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs – Bart C. Weimer – Frontiers in Microbiology

 

Animal Microbiome

The gut microbiota drives the impact of bile acids and fat source in diet on mouse metabolism – Sarah Just – Microbiome

Changes in feeding habits promoted the differentiation of the composition and function of gut microbiotas between domestic dogs (Canis lupus familiaris) and gray wolves (Canis lupus) – Tianshu Lyu – AMB Express

The effect of dietary lipid on gut microbiota in a senescence-accelerated prone mouse model (SAMP8) – Kazushi Yamamoto – Biogerontology

Moderate Dietary Protein Restriction Optimized Gut Microbiota and Mucosal Barrier in Growing Pig Model – Xiyue Chen – Frontiers in Cellular and Infection Microbiology

Effects of Sub-Chronic MPTP Exposure on Behavioral and Cognitive Performance and the Microbiome of Wild-Type and mGlu8 Knockout Female and Male Mice – Eileen Ruth S. Torres – Frontiers in Behavioral Neuroscience

Microbiota influence the development of the brain and behaviors in C57BL/6J mice – Jing Lu – PLoS ONE

Intestinal Microbiota Lipid Metabolism Varies across Rainbow Trout (Oncorhynchus mykiss) Phylogeographic Divide – Christina C. Yildirimer – Journal of Applied Microbiology

Chronic refined low-fat diet consumption reduces cholecystokinin satiation in rats – Mathilde Guerville – European Journal of Nutrition

The dynamics of the piglet gut microbiome during the weaning transition in association with health and nutrition – Robin B. Guevarra – Journal of Animal Science and Biotechnology

 

Methodologies

Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols – Cécile Angebault – PLoS ONE

 

Beneficial Microbes and Compounds

A prebiotic intervention study in children with autism spectrum disorders (ASDs) – Roberta Grimaldi – Microbiome

Chemical Compositions of Cold-pressed Broccoli, Carrot and Cucumber Seed Flours, and Their in Vitro Gut Microbiota Modulatory, Anti-inflammatory and Free Radical Scavenging Properties – Uyory Choe – Journal of Agricultural and Food Chemistry

 

Pathogen Research

Review: Nontuberculous Mycobacteria in Cystic Fibrosis – Brian S. Furukawa – Seminars in Respiratory and Critical Care Medicine