August 15, 2018

A nice crop of plant/root/soil microbiome studies, some interesting analyses of early life/pregnancy and vaginal microbiota, a belly-load of gut microbiome science, a herd of animal studies, and a few really bad puns… Enjoy!

Events and jobs

A summary of the third annual HIV microbiome workshop – Dr. Brett Williams – AIDS Research and Human Retroviruses

Pregnancy and early life

Early childhood antibiotics use and autism spectrum disorders: a population-based cohort study – Amani F Hamad – International Journal of Epidemiology

The effects of gut microbiota on metabolic outcomes in pregnant women and their offspring – You Lv – Food & Function

Human vaginal microbiome

Cervicovaginal microbiota, women’s health, and reproductive outcomes – Samuel J. Kroon – Fertility and Sterility

Relevance of assessing the uterine microbiota in infertility – Inmaculada Moreno – Fertility and Sterility

Cervicovaginal microbiota, women’s health, and reproductive outcomes – Samuel J. Kroon – Fertility and Sterility

Human nearly-sterile sites

Ursodeoxycholic acid improves liver function via phenylalanine/tyrosine pathway and microbiome remodelling in patients with liver dysfunction – Da Jung Kim – Scientific Reports

Human gut microbiome

Assessing antibiotic resistance gene load in vegan, vegetarian and omnivore human gut microbiota – Losasso Carmen – International Journal of Antimicrobial Agents

Immunomodulatory tetracyclines ameliorate DNBS-colitis: Impact on microRNA expression and microbiota composition – J. Garrido-Mesa – Biochemical Pharmacology

Effects of anthocyanins from the fruit of Lycium ruthenicum Murray on intestinal microbiota – Yamei Yan – Journal of Functional Foods

Disparate Effects of Antibiotics on Hypertension – Sarah Galla – Physiological Genomics

Variability of core microbiota in newly diagnosed treatment-naïve paediatric inflammatory bowel disease patients – T. G. J. de Meij – PLOS One

Dietary soybean protein ameliorates high-fat diet-induced obesity by modifying the gut microbiota-dependent biotransformation of bile acids – Keita Watanabe – PLOS One

Gut microbiota alterations in moderate to severe acne vulgaris patients – Hui‐Min Yan – The Journal of Dermatology

Implication of gut microbiota metabolites in cardiovascular and metabolic diseases – Francois Brial – Cellular and Molecular Life Sciences

Making Sense of… the Microbiome in Psychiatry – Thomaz F S Bastiaanssen – International Journal of Neuropsychopharmacology

The Microbiome in Cirrhosis and its Complications – Chathur Acharya – Clinical Gastroenterology and Hepatology

Lactobacillus rhamnosus GG induced protective effect on allergic airway inflammation is associated with gut microbiota – Juan Zhang – Cellular Immunology

The gut microbiome as a driver of individual variation in cognition and functional behaviour – Gabrielle L. Davidson – Philosophical Transactions of the Royal Society B

Animal experiments

The impact of Clostridium butyricum MIYAIRI 588 on the murine gut microbiome and colonic tissue – Mao Hagihara – Anaerobe

Monitoring and evaluation of the interaction between deoxynivalenol and gut microbiota in Wistar rats by mass spectrometry-based metabolomics and next-generation sequencing – Eugènia Miró-Abella – Food and Chemical Toxicology

Lentil (Lens culinaris Medikus) Diet Affects the Gut Microbiome and Obesity Markers in Rat – Niroshan Siva – Journal of Agricultural and Food Chemistry

Gut bacterial composition in a mouse model of Parkinson’s disease – P. Perez-Pardo – Beneficial Microbes

Gut Microbiome in BALB/c and C57BL/6J Mice Undergoing Experimental Thyroid Autoimmunity Associate with Differences in Immunological Responses and Thyroid Function – Sajad Moshkelgosha – Hormone and Metabolic Research

Ultraviolet Irradiation of Skin Alters the Faecal Microbiome Independently of Vitamin D in Mice – Simon Ghaly – Nutrients

Impact of lincosamides antibiotics on the composition of the rat gut microbiota and the metabolite profile of plasma and feces – C. Behr – Toxicology Letters

Animal microbiome

Understanding bacterial communities for informed biosecurity and improved larval survival in Pacific oysters – Olivier Laroche – Aquaculture

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota – Fernanda Cornejo-Granados​ – PeerJ

Do the microorganisms from laboratory culture spent growth medium affect house dust mite fitness and microbiome composition? – Vit Molva – Insect Science

Plant, root, and soil microbiome

Microbial diversity associated to the intestinal tract of soil invertebrates – Dayana da Silva Correia – Applied Soil Ecology

Yellow Canopy Syndrome in sugarcane is associated with shifts in the rhizosphere soil metagenome but not with overall soil microbial function – Kelly Hamonts – Soil Biology and Biochemistry

Anthropogenic influence shapes the distribution of antibiotic resistant bacteria (ARB) in the sediment of Sundarban estuary in India – Anish Bhattacharyya – Science of the Total Environment

Disentangling effects of temperature on microbial community and copper extraction in column bioleaching of low grade copper sulfide – Yuguang Wang – Bioresource Technology

Long-term Plastic Greenhouse Cultivation Changes Soil Microbial Community Structures: A Case Study – Yang Song – Journal of Agricultural and Food Chemistry

Flooding and prolonged drought have differential legacy impacts on soil nitrogen cycling, microbial communities and plant productivity – Linh T. T. Nguyen – Plant and Soil

[PhD Dissertation] Microbial Communities and Their Impact on Bioenergy Crops in Dynamic Environments – Brandon Monier, South Dakota State University – Open Prairie

[PDF] Characterization of osmotolerant rhizobacteria for plant growth promoting
activities in vitro and during plant-microbe association under osmotic stress – Bandeppa – Indian Journal of Experimental Biology

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments – Morgan R. McPherson – J. Vis. Exp

Water and extremophile microbiome 

[PDF download] Monitoring biofilm communities in operational drinking water distribution systems and the impact on water quality – I. Douterelo – 1st International WDSA

Molecular detection of microbial communities associated with Microcystis vs Synechococcus dominated waters in Tianjin, China – Da Huo – Journal of Oceanology and Limnology

Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia – Katherine Bedoya – Science of the Total Environment

Profiling microbial communities in a watershed undergoing intensive anthropogenic activities – Hehuan Liao – Science of the Total Environment

The gut microbiome and aquatic toxicology: An emerging concept for environmental health – Ondrej Adamovsky – PeerJ

Microbial community composition of a hydrocarbon reservoir 40 years after a CO2 enhanced oil recovery flood – Jenna L K Shelton – FEMS Microbiology Ecology

Temporal dynamics of activated sludge bacterial communities in two diversity variant full-scale sewage treatment plants – Xiao-Tao Jiang – Applied Microbiology and Biotechnology

The Nile River Microbiome Reveals a Remarkably Stable Community Between Wet and Dry Seasons, and Sampling Sites, in a Large Urban Metropolis (Cairo, Egypt) – Eraqi WA – OMICS

Probiotics / prebiotics

Influence of monostrain and multistrain probiotics on immunity, intestinal ultrastructure and microbiota in experimental dysbiosis – E. Ermolenko – Beneficial Microbes

Effects of Probiotics on Inflammation and Uremic Toxins Among Patients on Dialysis: A Systematic Review and Meta-Analysis – Charat Thongprayoon – Digestive Diseases and Sciences

Bioinformatics

Biomarker panels for characterizing microbial community biofilm formation as composite molecular process – Magnus Bosse – PLOS One

* Maximal viral information recovery from sequence data using VirMAP – Nadim J Ajami – Nature Communications

Techniques

Using Bioreactors to Study the Effects of Drugs on the Human Microbiota – Mabel Guzman-Rodriguez – Methods

Ed’s non-microbiology picks

Human activities might influence oncogenic processes in wild animal populations – Mathieu Giraudeau – Nature Ecology & Evolution

In apoptosis, cell death spreads through perpetuating waves – James Ferrell – Stanford Medicine

Study finds Tdap vaccination for pregnant women does not increase risk of autism

Boys should be given HPV vaccine, says joint committee

New Study: Omega-3s Can Help Keep Kids Out of Trouble

Mars (probably) has a lake of liquid water

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August 13, 2018

Today’s Digest is full of amazing research from focusing on causation in microbiome studies to increased efficacy of BLAST searches in the age of high throughput sequencing.

General Microbiome

Microbiome: Focus on Causation and Mechanism.Fischbach MA. Cell.

Effect of Antibiotic-Mediated Microbiome Modulation on Rotavirus Vaccine Immunogenicity: A Human, Randomized-Control Proof-of-Concept Trial.Harris VC. Cell Host and Microbe

Enhancing Rotavirus Vaccination: A Microbial Fix? Parker EPK. Cell Host and Microbe

Snapshot of an early Paleoproterozoic ecosystem: Two diverse microfossil communities from the Turee Creek Group, Western Australia. Barlow EV. Geobiology.

Background levels of microorganisms in the busy urban environment of transport hubs.Patel KV. Journal of Applied Microbiology.

Immunomodulation as Therapy for Fungal Infection: Are We Closer?Sam QH. Frontiers in Microbiology

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.Grahl N. mSphere.

Oral Microbiome

Comparison of oral microbiota in orthodontic patients and healthy individuals.Sun F. Microbial Pathogenesis

Skin Microbiome

Mud therapy and skin microbiome: a review.Antonelli M. International Journal of Biometeorology

Gut Microbiome

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.Bradley PH. PLoS Computational Biology

Dynamic changes in human-gut microbiome in relation to a placebo-controlled anthelminthic trial in Indonesia.Martin I. PLoS Neglected Tropical Disease.

Faecal Microbiome

Effects of metal and metalloid pollutants on the microbiota composition of feces obtained from twelve commercial pig farms across China.Peng Z. Science Total Environment

Fecal Microbiota Alterations Associated With Diarrhea-Predominant Irritable Bowel Syndrome.Zhuang X. Frontiers in Microbiology.

Plant, Soils, and Air Microbiome

Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils.Tang Y. Science of Total Environment

Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa. Kumar V. PLoS One.

Trichoderma polysporum selectively inhibits white-nose syndrome fungal pathogen Pseudogymnoascus destructans amidst soil microbes.Singh A. Microbiome.

Tissue Microbiome of Norway Spruce Affected by Heterobasidion-Induced Wood Decay.Ren F. Microbial Ecology

Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments. Yu C. Applied Microbiology and Biotechnology.

Traits-Based Integration of Multi-Species Inoculants Facilitates Shifts of Indigenous Soil Bacterial Community.Wang J. Frontier in Microbiology

Spatial Patterns and Drivers of Microbial Taxa in a Karst Broadleaf Forest.Song M. Frontiers in Microbiology

Water Microbiome

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.Berner C. Frontiers in Microbiology

Coral Microbiome Database: Integration of sequences reveals high diversity and relatedness of coral-associated microbes.Huggett MJ. Environmental Microbiology Reports

Animal Experiments and Microbiome

Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake. Kashinskaya EN. Journal of Applied Microbiology

Yeast-like microorganisms in the scale insect Kermes quercus (Insecta, Hemiptera, Coccomorpha: Kermesidae). Newly acquired symbionts?Podsiadło E. Arthropod Structure and Development

Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population.Leis ML. Veterinary Ophthalmology

High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer (<i>Moschus berezovskii</i>).Hu X. Frontiers in Microbiology

A Comprehensive Research on Antibiotic Resistance Genes in Microbiota of Aquatic Animals.Hong B. Frontiers in Microbiology

Identification of spider-mite species and their endosymbionts using multiplex PCR.Zélé F. Experimental and Applied Acarology

Soil microarthropods alter the outcome of plant-soil feedback experiments.Kuťáková E. Scientific Reports

Techniques/Bioinformatics 

Metagenome complexity and template length are the main causes of bias in PCR-based bacteria community analysis.Peng W. Journal of Basic Microbiology

Single-cell RNA sequencing technologies and bioinformatics pipelines.Hwang B. Experimental and Molecular Medicine

Negative Binomial Mixed Models for Analyzing Longitudinal Microbiome Data.Zhang X. Frontiers in Microbiology

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems. Hu Y. Scientific Reports

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.Tristão Ramos RJ. Bioinformatics

23 July, 2018

Today’s digest includes exciting Microbiome events and brilliant papers on animal microbiomes. Lastly, research exploring the war on gluten.

Events

Microbiome X Regulation 1 Panel discussion on navigating the FDA

Introduction to the 4th International Symposium on Gluten-Free Cereal Products and Beverages.

General Microbiome

Antibiotic Scars Left on the Gut Microbiota from the Stringent Response. Yi H. Trends in Microbiology

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Hua ZS. Nature Communications

Genomic Characterization of Sulphite Reducing Bacteria Isolated From the Dairy Production Chain.Doyle CJ. Frontiers in Microbiology.

How Microbial Aggregates Protect against Nanoparticle Toxicity.Tang J. Trends in Biotechnology.

Inhibition of microbial spoilage of grass carp (Ctenopharyngodon idellus) fillets with a chitosan-based coating during refrigerated storage. Yu D. International Journal of Food Microbiology

Gut Microbiome

The gut microbiome and irritable bowel syndrome. Menees S. F1000Research

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism.Zarrinpar A. Nature Communications

Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Zhang X. Nature Communications

Techniques

A rapid PCR-based method to discriminate Macrococcus caseolyticus and Macrococcus canis from closely-related Staphylococcus species based on the ctaC gene sequence. Mazhar S. Journal of Microbiological Methods

MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification. Vervier K. Methods in Molecular Biology

Soil, Water, and Air Microbiome

Influence of new agromining cropping systems on soil bacterial diversity and the physico-chemical characteristics of an ultramafic soil. Saad RF. Science of the Total Environment

<i>Pseudomonas chlororaphis</i> produces multiple R-tailocin particles that broaden the killing spectrum and contribute to persistence in rhizosphere communities.Dorosky RJ. Applied and Environmental Microbiology

REVIEW: Microbial diversity and biogeography in Arctic soils.Malard LA. Environmental Microbiology Reports.

Impact of brine and antiscalants on reef-building corals in the Gulf of Aqaba – Potential effects from desalination plants.Petersen KL. Water Research

Mapping the Bacterial Community in Digboi Oil Refinery, India by High-Throughput Sequencing Approach. Dasgupta A.  Current Microbiology.

Chemical-, site-, and taxa-dependent benthic community health in coastal areas of the Bohai Sea and northern Yellow Sea: A sediment quality triad approach. Khim JS. Science of the Total Environment.

Animal Experiments and Microbiome

Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda. Zeng Y. Frontiers in Microbiology

REVIEW:The gut microbiota of wild rodents: Challenges and opportunities. Viney M. Laboratory Animals

Genome-wide association studies of inflammatory bowel disease in German shepherd dogs. Peiravan A. PLoS One.

Effects of Rodent Diet Choice and Fiber Type on Data Interpretation of Gut Microbiome and Metabolic Disease Research.Pellizzon MA. Current Protocols in Toxicology

Non-Microbiology Hot Pick

The war on gluten. Servick K. Science.

 

 

July 8, 2018

Today’s Microbiome Digest blog comes up with the current research articles on the microbiome of GIT, Respiratory, UT, Vagina, Infant, Oral, Marine, Plant-Soil and Animal- Bird. It also features the articles on the bioremediation, pre/pro-biotics, nutrient and dietary effects on microbiome, the potential prognosis, biofilm reduction and multi-omics study of pregnancy cohort, role of Environmental Contaminants(ECs), spore-forming bacteria, attenuation of colitis score, systematic repercussions by antibiotics, glucocorticoid signaling, TMAO, drug-induced liver injury (DILI), neurotransmitter interactions, effect of glycation of fish proteins, NOD2-IBD, Carbapenemase-producing Enterobacteriaceae (CPE).

Have a look and enjoy SUNDAY!

EVENTS, JOBS, PhD POSITIONS:

EVENT – Third Annual Microbiome Symposium on September 24 , 8:00AM – 7:00PM at the Stanford Faculty Club

 

GASTRO-INTESTINAL MICROBIOME: 

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas – Bhabatosh Das – Scientific Reports 

Review – The Mammalian Intestinal Microbiome: Composition, Interaction with the Immune System, Significance for Vaccine Efficacy, and Potential for Disease Therapy – Desselberger U – Pathogens

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients – Bahtiyar Yilmaz – PLoS One

Absence of NOD2 receptor predisposes to intestinal inflammation by a deregulation in the immune response in hosts that are unable to control gut dysbiosis – Patrícia Reisde Souza – Immunobiology

Review – Outside the liver box: The gut microbiota as pivotal modulator of liver diseases – Annika Wahlström – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

 

RESPIRATORY MICROBIOME:

Review – Microbiome in the primary prevention of allergic diseases and bronchial asthma – B.Sozańska – Allergologia et Immunopathologia

Severe Obstructive Sleep Apnea is Associated with Alterations in the Nasal Microbiome and Increase in Inflammation – Benjamin G Wu – American Journal of Respiratory and Critical Care Medicine

URINARY TRACT MICROBIOME:

Review – Infections – The Urinary Tract Microbiome: The Answer to All Our Open Questions? – Giuseppe Magistro – European Urology focus

VAGINAL MICROBIOME:

Anti-HIV-1 Activity of Lactic Acid in Human Cervicovaginal Fluid – Tyssen D – mSphere

INFANT MICROBIOME:

Bifidobacterium longum subsp. infantis EVC001 stably restores the infant gut microbiome over the first year of life in breastfed infants – Jennifer Smilowitz – Pediatrics

Review – Does antibiotic choice for the treatment of suspected late-onset sepsis in premature infants determine the risk of developing necrotising enterocolitis? A systematic review – Josephine V.Seale – Early Human Developmment

ORAL MICROBIOME: 

Review – Cariogenic microbiome and microbiota of the early primary dentition: a contemporary overview – Fakhruddin KS – Oral Diseases

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin – Mann AE – Scientific Reports

Distinctions and associations between the microbiota of saliva and supragingival plaque of permanent and deciduous teeth – Shi W – PLoS One

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease – Kazumichi Abe – PLoS One

GENERAL HUMAN MICROBIOME:

Human-associated microbial populations as evidence in forensic casework – Frederike C.A – Forensic Science International: Genetics

Book chapter – Genomics and Drug-Metabolizing Enzymes and Its Application in Drug Delivery: Evaluating the Influence of the Microbiome – Sheeba Varghese Gupta

Effects of Substance Use and Sex Practices on the Intestinal Microbiome During HIV-1 Infection – Jennifer A Fulcher –The Journal of Infectious Diseases

Preview – Interactions between Clostridioides difficile and fecal microbiota in in vitro batch model: growth, sporulation and microbiota changes – Sabina Horvat – Frontiers in Microbiology

Review – Metagenomic and clinical microbiology – Sophie Amrane – Human Microbiome

Implants induce a new niche for microbiomes – Tim H. Jakobsen – Wiley Online Library

Short Communication Transmission of IMI-2 carbapenemase-producing Enterobacteriaceae from river water to human – Chrislène Laurens – Journal of Global Antimicrobial Resistance

Review – The hygiene hypothesis: immunological mechanisms of airway tolerance – Eline Haspeslagh – Current Opinion in Immunology

Microbiota affects the expression of genes involved in HPA axis regulation and local metabolism of glucocorticoids in chronic psychosocial stress – M. Vodička – Brain, Behavior, and Immunity

Review – The Role of Microbiota in Cardiovascular Risk: Focus on Trimethylamine Oxide – HusseinAl-Rubaye – Current Problems in Cardiology

 

HUMAN-MICROBE CROSS-TALK:

Gut Microbiota-Dependent Trimethylamine N-Oxide Predicts Risk of Cardiovascular Events in Patients With Stroke and Is Related to Proinflammatory Monocytes – Haghikia A – Arterioscler Thromb Vasc Biol.

Cutting Edge: Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism – Catherine R. Lammert – J Immunol

Critical Role for the Microbiota in CX3CR1+ Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses – Myunghoo Kim – Immunity

 

MARINE/WATER MICROBIAL ECOLOGY:

Review – Ecology and evolution of seafloor and subseafloor microbial communities – WD Orsi – Nature Reviews Microbiology

Metabolic potential of microbial communities from ferruginous sediments – Aurèle Vuillemin – Environmental Microbiology

Metagenomic analysis of basal ice from an Alaskan glacier – Kayani MUR – Microbiome

Patterns of Change in Metabolic Capabilities of Sediment Microbial Communities in River and Lake Ecosystems – Oest A1 – Int J Microbiol

Succession of toxicity and microbiota in hydraulic fracturing flowback and produced water in the Denver–Julesburg Basin – Natalie M Hull – Science of The Total Environment

 

PLANT or SOIL MICROBIOME:

Preview – New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes – Marie E. Kroeger – Frontiers in Microbiology

Litter quality drives the differentiation of microbial communities in the litter horizon across an alpine treeline ecotone in the eastern Tibetan Plateau – Haifeng Zheng – Scientific Reports

Preview – Unravelling the composition of the root-associated bacterial microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology

 

BIOREMEDIATION:

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor – Nsanzumukiza Martin Vincent – Int. J. Environ. Res. Public Health

Review – Response of microbial communities to oil spill in the Gulf of Mexico: A review – Linda Adzigbli – Afr. J. Microbiol. Res

A two-staged system to generate electricity in microbial fuel cells using methane – Jaewook Myung – Chemical Engineering Journal

The influence of pressure on crude oil biodegradation in shallow and deep Gulf of Mexico sediments – Nguyen UT – PLoS One

Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers – Robert E. Danczak – mSystems

Energy efficiency: Importance of indigenous microorganisms contained in the municipal solid wastes – S.Zahedi – Waste management

Systematic characterization and proposed pathway of tetracycline degradation in solid waste treatment by Hermetia illucens with intestinal microbiota – Minmin Cai – Environmental Pollution

 

NUTRITION or DIET and TREATMENTS:

Functional Effects of the Buckwheat Iminosugar d-Fagomine on Rats with Diet-Induced Prediabetes – Ramos-Romero S – Mol Nutr Food Res

Long-Term Genistein Consumption Modifies Gut Microbiota, Improving Glucose Metabolism, Metabolic Endotoxaemia and Cognitive Function in Mice Fed a High-Fat Diet – López P – Mol Nutr Food Res

Brown rice-specific γ-oryzanol as a promising prophylactic avenue to protect against diabetes mellitus and obesity disease in humans – Masuzaki H – J Diabetes Investig

Intestinal Inflammation in Chilean Infants Fed With Bovine Formula vs. Breast Milk and Its Association With Their Gut Microbiota – Ossa JC – Front Cell Infect Microbiol.

Trigonelline inhibits intestinal microbial metabolism of choline and its associated cardiovascular risk – Anwar S – J Pharm Biomed Anal

Off-target effects of tribendimidine, tribendimidine plus ivermectin, tribendimidine plus oxantel-pamoate, and albendazole plus oxantel-pamoate on the human gut microbiota – Pierre H.H.Schneeberger – International Journal for Parasitology: Drugs and Drug Resistance

Isoquercetin and inulin synergistically modulate the gut microbiome to prevent development of the metabolic syndrome in mice fed a high fat diet – Si Tan – Scientific Reports

Glycation of fish protein impacts its fermentation metabolites and gut microbiota during in vitro human colonic fermentation – Yuhong Yang – Food Research International

Correlation between microbiota and flavours in fermentation of Chinese Sichuan Paocai – YangshengXiao – Food Research International

Review – Relationship between fatty acids intake and Clostridium coccoides in obese individuals with metabolic syndrome – Giovana Jamar – Food Research International

Review – Microbiota of milk powders and the heat resistance and spoilage potential of aerobic spore-forming bacteria – Faizan A.Sadiq – International Diary Journal

Review – The debate over neurotransmitter interaction in aspartame usage – Arbind Kumar Choudhary – Journal of Clinical Neuroscience

 

METHODS:

Reevaluating approaches to cystic fibrosis pulmonary exacerbations – Schechter MS – Pediatr Pulmonol

Review – Bioresponsive drug delivery systems in intestinal inflammation: State-of-the-art and future perspectives – Niranjan G.Kotla – Advance Drug Delivery Reviews

Rapid analysis of photoautotroph microbial communities in soils by flow cytometric barcoding and fingerprinting – László Menyhárt – Applied Soil Ecology

Degradation studies of modified inulin as potential encapsulation material for colon targeting and release of mesalamine – MichaelWalz – Carbohydrate Polymers

Review – Advances in drug-induced cholestasis: Clinical perspectives, potential mechanisms and in vitro systems – M. LeonorFernández-Murga – Food and Chemical Toxicology

 

ANIMAL and BIRD MICROBIOME:

Characteristics of microbial communities and intestinal pathogenic bacteria for migrated Larus ridibundus in southwest China – Liao F – Microbiology Open

Gut microbiota correlates with fiber and apparent nutrients digestion in goose – Guojun Liu – Poultry Science

Feeding sows resistant starch during gestation and lactation impacts their faecal microbiota and milk composition but shows limited effects on their progeny – Julie Leblois – PLoS One

Analysis of temporal fecal microbiota dynamics in weaner pigs with and without exposure to enterotoxigenic Escherichia coli – J. Pollock – Journal of Animal Science

 

ANIMAL EXPERIMENTS:

Aryl hydrocarbon receptor/IL-22/Stat3 signaling pathway is involved in the modulation of intestinal mucosa antimicrobial molecules by commensal microbiota in mice – Wang J – Innate Immun.

Oral infection of mice with Fusobacterium nucleatum results in macrophage recruitment to the dental pulp and bone resorption – Larry Johnson – Biomedical Journal

Preview – Fecal Microbiota Transplantation is Associated with Reduced Morbidity and Mortality in Porcine Circovirus Associated Disease – Megan C. Niederwerder – Frontiers in Microbiology

Oral treatment with Lactobacillus rhamnosus 64 during the early postnatal period improves the health of adult rats with TNBS-induced colitis – Stanislava Stanojević – Journal of Functional Foods

Antibiotic-induced dysbiosis effects on the murine gastrointestinal tract and their systemic repercussions – Caio PupinRosa – Life Sciences

 

MICROBIOLOGY:

N-Acetyl-glucosamine influences the biofilm formation of Escherichia coli – Sicard JF – Gut Pathog

Benzoyl Peroxide Inhibits Quorum Sensing and Biofilm Formation by Gardnerella vaginalis 14018 – Ammar Algburi – Infectious Diseases in Obstetrics and Gynecology

 

PRE/PRO – BIOTICS:

Review : Benefaction of probiotics for human health: A review – George Kerry R – J Food Drug Anal

Review – Role of prebiotics in regulation of microbiota and prevention of obesity – Grethel T.Choque Delgado – Food Research International

Effects of the Administration of Probiotics on Fecal Microbiota Diversity and Composition in Healthy Individuals – Choong-Kyun Noh – J Neurogastroenterol Motil

 

METABOLOMICS:

Microbiome-related metabolite changes in gut tissue, cecum content and feces of rats treated with antibiotics – C.Behr – Toxicology and Applied Pharmacology

 

MULTI-OMICS PICKS:

Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Human Pregnancy – Mohammad Sajjad Ghaemi – Bioinformatics

July 5, 2018

Today’s microbiology picks have articles on sampling source effect on the gut microbial diversity, whether resistant starch in mothers could benefit the offsprings, protective role of the gut bacteria of firebugs, microbial community shift during different stages in anaerobic membrane bioreactor, NanoAmpli-Seq as well as articles from plant-root-soil microbiome. Precision medicine, genetics of social interaction and isolation, “ethics dumping ” among our non-microbiology picks.

 

Events and jobs

John Maddox Prize 2018 nomination – Deadline: 13th August 2018 – Check their website for more details

General microbiome

Human-associated microbial populations as evidence in forensic casework – Frederike C.A. Quaak – Forensic Science International: Genetics

The Mammalian Intestinal Microbiome: Composition, Interaction with the Immune System, Significance for Vaccine Efficacy, and Potential for Disease Therapy.  – U Desselberger – MDPI

244 Analysis of microbiome prostatic secretion in depending of levels total testosterone in blood serum – M.I. Kogan – The Journal of Sexual Medicine

Triclosan and triclocarban exposure, infectious disease symptoms and antibiotic prescription in infants—A community-based randomized intervention – Catherine Ley – PLoS One

 

Human skin microbiome

Microbiome analysis of forehead skin in patients with atopic dermatitis and healthy subjects: Implication of Staphylococcus and Corynebacterium –  Masutaka Furue – The Journal of Dermatology

Human vaginal microbiome

Trichomonas vaginalis: Pathogenesis, Symbiont Interactions, and Host Cell Immune Responses – Frances Mercer – Trends in Parasitology

Human gut microbiome

More of the Gut in the Lung: How Two Microbiomes Meet in ARDS – Samiran Mukherjee – Yale Journal of Biology and Medicine

The Influence of Gut Microbial Metabolism on the Development and Progression of Non-alcoholic Fatty Liver Disease – Wei Jia – Obesity, Fatty Liver and Liver Cancer

Severe Defects in the Macrophage Barrier to Gut Microflora in Inflammatory Bowel Disease and Colon Cancer. – Carlos A. Rubiro – Anticancer Research

Animal experiments 

Feeding sows resistant starch during gestation and lactation impacts their faecal microbiota and milk composition but shows limited effects on their progeny – Julie Leblois – PLoS One

Animal microbiome

The cotton stainer’s gut microbiota suppresses infection of a co‐transmitted trypanosomatid parasite – Thomas O Onchuru – Molecular Ecology

Gut microbial diversity in two insectivorous bats: Insights into the effect of different sampling sources – Haonan Wu – Microbiology Open

Evidence for multiple ecological roles of Leptographium abietinum, a symbiotic fungus associated with the North American spruce beetle – Thomas S Davis – Fungal Ecology

Plant, root, and soil microbiome

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon – Evan P Starr – Microbiome

Swift Acid Rain Sensing by Synergistic Rhizospheric Bioelectrochemical Responses – Tian Li – ACS Sensors

Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays – Saarah A Maarastawi – Frontiers in Microbiology

Plant growth promoting bacteria associated with corm of Crocus sativus during three growth stages – Ranjit Kour – Letters in Applied Microbiology

Fungal Diversity of Rhizosphere Soil from 11 Varieties of Grapevines at Maturity Stage from Two Vineyards in China – Ping Zhao – Journal of Biobased Materials and Bioenergy

Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates – Meike Siebers – PLoS One

The value of wet leaves – Todd E. Dawson – New Phytologist

Water and extremophile microbiome 

Biofilm and planktonic bacterial communities in a drinking water distribution system supplied with untreated groundwater – Jianfei Chen – Archives of Microbiology

Marine Environmental Epigenetics – Jose M. Eirin-Lopez – Annual Reviews

Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration ratesDisentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates – Oliver Müller – Environmental Microbiology

Effect of different carbon sources on denitrification performance, microbial community structure and denitrification genes – Zhongshuo Xu – Science of The Total Environment

Built environment 

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor –  Nsanzumukiza Martin Vincent – MDPI

Food microbiology

Inactivation of Escherichia coli O157:H7 and Salmonella and Native Microbiota on Fresh Strawberries by Antimicrobial Washing and Coating – Mingming Guo – Journal of Food Protection

Microbial quality of ice cream sold by retail outlets in Erzurum. –  S Çubukçı – CAB Direct

 

Techniques

Preprint: NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform – Szymon T Calus – bioRxiv

Preprint: Genetic insight into zinc and antimicrobial toxicity uncovers a glycerol phosphate modification on streptococcal rhamnose polysaccharides – Rebecca J. Edgar – bioRxiv

Preprint: Nano-particles from Chaetomium against Rice Blast – Jiao Jiao Song – bioRxiv

Seamless assembly of recombinant adenoviral genomes from high-copy plasmids – Jessica J. Miciak – PLoS One

Twenty-seven years of screening for Shiga toxin-producing Escherichia coli in a university hospital. Brussels, Belgium, 1987-2014 – Klara De Rauw – PLoS One

Microbes in the news

Bacteria Fight Competitors by Turning them Against Each Other – Technology Networks

Non-microbiology Picks

Personalized medicine should not be restricted to the wealthy – Nature

Elucidating the genetic basis of social interaction and isolation – Nature Communications

Evaluation woes: we’re on it, responds DORA – Nature

Italy is squeezing out wet biology research – Nature

Europe’s biggest research fund cracks down on ‘ethics dumping’ – Nature

 

July 02, 2018

Good morning! Today’s Microbiome Digest will cover the general microbiome, HIV infection and multi-site bacterial microbiota, crucial role of lung microbiome in asthma, gut microbiome in type 1 diabetes, Link between diet and metabolic syndrome, Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes, HmmUFOtu: a tool for taxonomic assignment and OTU picking and a news on plastic eating bacteria …

Events and jobs

Post-Doctoral Research Position, Oregon State University, with Dr. Stephen Giovannoni

Postdoctoral Researcher Position Characterizing Microbial Candidate Phlya at Stanford University

General microbiome

Issue: The microbiome: more than a gut reaction – John R. Wingard – Blood

Evaluation at scale of microbiome-derived metabolites as biomarker of flavan-3-ol intake in epidemiological studies – Javier I. Ottaviani – Scientific Reports

All disease begins in the gut: Influence of gastrointestinal disorders and surgery on oral drug performance – Grace B. Hatton – International Journal of Pharmaceutics

Designing microbial consortia with defined social interactions – Wentao Kong – Nature Chemical Biology

Multi-site human microbiome

HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa – Heidi Tuominen – Scientific Reports

Human respiratory microbiome

State of the Art: Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human vaginal microbiome

Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth – Aline C. Freitas – Microbiome

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes Metab Res Rev

Review: Altered Gut Microbiota: A Link Between Diet and the Metabolic Syndrome – Velasquez Manuel T – Metabolic Syndrome and Related Disorders

Chapter: Microbiota, Obesity and NAFLD – Louis H. S. Lau – Obesity, Fatty Liver and Liver Cancer

Chapter: The Influence of Gut Microbial Metabolism on the Development and Progression of Non-alcoholic Fatty Liver Disease – Wei Jia – Obesity, Fatty Liver and Liver Cancer

Method: Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Ancient Thali Diet: Gut Microbiota, Immunity, and Health – Kaitlyn Shondelmyer – Yale Journal of Biology & Medicine

Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet – Yunjian Zhang – Epilepsy Research

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut – Whitman B. Schofield – Cell Host & Microbe

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Review: The Gut Microbiome Alterations and Inflammation-Driven Pathogenesis of Alzheimer’s Disease—a Critical Review – Marta Sochocka – Molecular Neurobiology

The controversial role of Enterococcus faecalis in colorectal cancer – Carolina Vieira de Almeida – Therapeutic Advances in Gastroenterology

Animal experiments

Pea-protein alginate encapsulation adversely effects development of clinical signs of Citrobacter rodentium-induced colitis in mice treated with probiotics – Natallia Varankovich – Canadian Journal of Microbiology

Maternal Soluble Fiber Diet during Pregnancy Changes the Intestinal Microbiota, Improves Growth Performance, and Reduces Intestinal Permeability in Piglets – Chuanshang Cheng – Applied and Environmental Microbiology

Overlapping community composition of gut and fecal microbiomes in lab-reared and field-collected German cockroaches – Madhavi L. Kakumanu – Applied and Environmental Microbiology

TRIF deficiency protects non-obese diabetic mice from type 1 diabetes by modulating the gut microbiota and dendritic cells – Elke Gülden – Journal of Autoimmunity

Mucosal homeostasis is altered in the ileum of gnotobiotic mice – Chasen J. Greig – Journal of Surgical Research

Animal microbiome

Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire – Jan F. Gogarten – The ISME Journal

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes – Pablo Tsukayama – mSystems

Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian – Sarah M. Griffiths – The ISME Journal

Plant, root, and soil microbiome

Review: Multifaceted Impacts of Bacteriophages in the Plant Microbiome – Britt Koskella – Annual Review of Phytopathology

‘Concord’ grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes – R.W.Lewis – Plant Physiology and Biochemistry

Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil – Mobolaji F. Adegboye – Genome Announcements

Differences in microbial key players in anaerobic degradation between biogas and sewage treatment plants – Christian Buettner – International Biodeterioration & Biodegradation

Water and extremophile microbiome

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico – Leila J. Hamdan – Scientific Reports

Stoichio-Metagenomics of ocean waters: a molecular evolution approach to trace the dynamics of nitrogen conservation in natural communities – Hannes Dittberner – Frontiers in Microbiology

 Probiotics / prebiotics

Review: Impact of Prebiotics on Poultry Production and Food Safety – Steven C. Ricke – Yale Journal of Biology & Medicine

Isolation and Partial Characterization of Lactic Acid Bacteria from the Gut Microbiota of Marine Fishes for Potential Application as Probiotics in Aquaculture – Sergio Alonso – Probiotics and Antimicrobial Proteins

Effects of Prebiotics vs a Diet Low in Fodmaps in Patients with Functional Gut Disorder – Jose-Walter Huaman – Gastroenterology

Bioinformatics

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies – Qi Zheng – Genome Biology

Techniques

Review: Culturing the human microbiota and culturomics – Jean-Christophe Lagier – Nature Reviews Microbiology

Microbes in the news

Plastic-eating bacteria discovered by student could help solve global pollution crisis

Sewage microbes make a fuel booster

Our intestinal microbiome influences metabolism — through the immune system

 

Ashok’s non-microbiology picks

Efficacy and Safety of Dupilumab in Glucocorticoid-Dependent Severe Asthma – Klaus F. Rabe – The NEW ENGLAND JOURNAL of Medicine

June 26, 2018

Today’s Microbiome Digest cover the topics on bioinformatics; methods and models; trials and therapies; infection and immunity; microbiome of human gut, human vagina, insect, animals, plant, marine; food and nutrition; bioremediation and metabolomics.

 

EVENTS- JOBS – PhD POSITIONS:

Event – Organoids: Modelling Organ Development and Disease in 3D Culture – EMBO| EMBL Symposia

 

NEWS and VIEWS:

Pairing off: a bottom-up approach to the human gut microbiome– Clare Abreu – Molecular Systems Biology

 

BIOINFORMATICS:
Zero-inflated generalized Dirichlet multinomial regression model for microbiome compositional data analysis – Tang ZZ – Biostatistics

 

METHODS and MODELS:

Book Chapter – Methods for Microbiota Analysis: Sample Collection and Laboratory Methods – Saleh Ibrahim – The Microbiome in Rheumatic Diseases and Infection

Review: Culturing the human microbiota and culturomics – Lagier JC – Nature Reviews Microbiology

Using glycolysis enzyme sequences to inform Lactobacillus phylogeny – Katelyn Brandt – Microbial Genomics

Multicenter study establishing the clinical validity of a nucleic-acid amplification-based assay for the diagnosis of bacterial vaginosis – Cartwright CP – Diagnostics Microbiology and Infectious Disease.

PATENT – SYSTEM AND METHODS FOR DEVELOPING AND USING A MICROBIOME-BASED ACTION COMPONENT FOR PATIENT HEALTH – Warren Tracy, Jantzen Tammi Gregory Katherine

 

TRIALS and THERAPIES:

Antimicrobial photodynamic therapy as a new approach for the treatment of vulvovaginal candidiasis: preliminary results – Aline Silva Sousa – Lasers in Medical Science

Review – Prevention of Cystitis: Travelling between the Imaginary and Reality – Vecchio M – Annals of Nutrition and Metabolism

 

INFECTIONS and IMMUNITY:

Book Chapter – The Impact of Infections on Reproduction and Fertility – VE Jones – Clinical Reproductive Science

Intestinal barrier disruption and dysregulated mucosal immunity contribute to kidney fibrosis in chronic kidney disease – Yang J – Nephrology Dialysis Transplantation

In Press: Treatment and Prevention of Recurrent Lower Urinary Tract Infections in Women: A Rapid Review with Practice Recommendations – Ariana l Smith – The Journal of Urology

Book Chapter – Immunology of the Microbiome: Implications for Rheumatoid Arthritis and Other Autoimmune Diseases – Daniel M Altmann – The Microbiome in Rheumatic Diseases and Infection

 

VAGINAL MICROBIOME:

Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov. – Diop K – Microbiology Open

 

GUT MICROBIOME: 

Preview – Gut microbiota as a missing link between nutrients and traits of human – Hea-Jong Chung – Frontiers in Microbiology

Preview – The gut-brain axis, the human gut microbiota and their integration in the development of obesity – Edward S Bliss – Frontiers in Microbiology

Review – The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes – Ömrüm Aydin – Current Diabetes reports

Beneficial metabolic effects of 2’, 3’, 5’-tri-acetyl-N6-(3-hydroxylaniline) adenosine in multiple biological matrices and intestinal flora of hyperlipidemic hamsters– Tianqi Li – Journal of Proteome Research

 

ANIMAL MICROBIOME:

Preview – Dynamics of gut microbiota diversity during the early development of an avian host: evidence from a cross-foster experiment – Aimeric Teyssier – Frontiers in Microbiology

Enterococcus faecium WEFA23 from infant lessens high-fat-diet-induced hyperlipidemia via cholesterol 7-alpha-hydroxylase gene by altering the composition of gut microbiota in rats – Fuqing Huang – ScienceDirect

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs – Flancman R – PloS One

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing – Ramesh J Pandit – Microbiome

 

GENERAL MICROBIOME:

Review – Role of nutrition, infection, and the microbiota in the efficacy of oral vaccines – Amrita Bhattacharjee – Clinical Science

Commensal Microbiota Enhance Both Osteoclast and Osteoblast Activities – Yoko Uchida – Molecules

 

PLANT/ROOT/SOIL MICROBIOME:

Editorial – The contribution of plant microbiota to economy growth – Angela Sessitsch – Microbial Biotechnology

Colonization cues of leaf- and root-inhabiting bacterial microbiota of Atractylodes lancea derived in vitro and in vivo – Yong Jia – Plant and Soil

Preview – Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism – Yuanchan Luo – – Frontiers in Microbiology

Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a HighSalinity Environment – Juan Ignacio Vílchez – GenomeAnnouncements

 

INSECT MICROBIOME:

Exposure of soil collembolans to microplastics perturbs their gut microbiota and alters their isotopic composition – DongZhu – Soil Biology and Biochemistry

 

SKIN MICROBIOME:

Book Chapter – Psoriasis and Psoriatic Arthritis – Madhura Castelino – The Microbiome in Rheumatic Diseases and Infection

 

MARINE MICROBIOME:
Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses – Felipe Hernandes Coutinho – Trends in Microbiology

 

NEONATAL/INFANT MICROBIOME:

Communication – Maternal Intrapartum Antibiotic Administration and Infantile Colic: Is there a Connection? – Leppälehto E – Neonatology

Review – Intrauterine Inflammation, Epigenetics, and Microbiome Influences on Preterm Infant Health – Lu L – Current Pathobiology Reports

 

CROSS – POPULATION MICROBIOME:
Similarities and differences in gut microbiome composition correlate with dietary patterns of Indian and Chinese adults – Abhishek Jain – AMB Express

 

PHAGES/VIRUSES:

Genome Sequence of the Pseudomonas protegens Phage GP100 – Jordan Vacheron – GenomeAnnouncements

 

FOOD and NUTRITION:

Plasma and urine metabolite profiling reveals the protective effect of Clinacanthus nutans in an ovalbumin-induced anaphylaxis model: 1H-NMR metabolomics approach – Leng Wei Khoo – Journal of Pharmaceutical and Biomedical Analysis

Drivers that establish and assembly the lactic acid bacteria biota in cheeses – Marco Gobbetti – Trends in Food Science & Technology

The food safety of DP-356Ø43 soybeans on SD rats reflected by physiological variables and fecal microbiota during a 90-day feeding study – Zou S – Regul Toxicol Pharmacol

Fermented Soybean Suppresses Visceral Fat Accumulation in Mice – Kushida M – Molecular Nutrition and Food Research

Combined Use of C. butyricum Sx-01 and L. salivarius C-1-3 Improves Intestinal Health and Reduces the Amount of Lipids in Serum via Modulation of Gut Microbiota in Mice – Long M – Nutrients

Review – Dietary polyphenols: A novel strategy to modulate microbiota-gut-brain axis – Diana Serra – Trends in Food Science & Technology

 

METABOLOMICS:

Non-invasive urinary metabolomic profiles discriminate biliary atresia from infantile hepatitis syndrome – Wei-Wei Li – Metabolomics

Metabolomics of the amniotic fluid: Is it a feasible approach to evaluate the safety of Chinese medicine during pregnancy? – Jinjun Shan – Journal of Applied Toxicology

Article – A validated, fast method for quantification of sterols and gut microbiome derived 5α/β-stanols in human faeces by isotope dilution LC-high resolution MS – Schoett HF – Analytical Chemistry

 

BIOREMEDIATION:

Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing – Mariela Beatriz Reyes-Sosa – Science of The Total Environment

 

ANTIBIOTIC SUSCEPTIBILITY:
Skin and nasal vestibule colonisation by Staphylococcus aureus and its susceptibility to drugs in atopic dermatitis patients – Wrobel J – Annals of Agriculture and Environmental Medicine