4 October, 2018

Today’s digest is full of exciting wine and animal microbiome studies!ūüėĀūüźĆūüć∑

General Microbiome

Editorial: Microbe and host lipids.Nigou J. Biochimie

Obesity alters composition and diversity of the oral microbiota in patients with type 2 diabetes mellitus independently of glycemic control.Tam J. PLoS One

Impact of the preoperative use of synbiotics in colorectal cancer patients: A prospective, randomized, double-blind, placebo-controlled study. Polakowski CB

The time response of anaerobic digestion microbiome during an organic loading rate shock. Braz GHR. Applied Microbiology and Biotechnology

REVIEW: Childhood weight gain and oral microbiota.Greenhill C. Nature Reviews Endocrinology

Glycan recognition at the saliva – Oral microbiome interface.Cross BW, Ruhl S. Cellular Immunology.

Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis. Lueschow SR. PLoS One

Direct Utilization of Organic Nitrogen by Phytoplankton and Its Role in Nitrogen Cycling Within the Southern California Bight. Morando M. Frontiers in Microbiology.

Persistence and reversal of plasmid-mediated antibiotic resistance.Lopatkin AJ. Nature Communications

Gut Microbiome

REVIEW: Effects of Metabolites Derived From Gut Microbiota and Hosts on Pathogens.Li Z.Frontiers in Cellular and Infection Microbiology

Food and Wine Microbiome

The effect of sulfur dioxide addition at crush on the fungal and bacterial communities and the sensory attributes of Pinot gris wines. Morgan SC. International Journal of Food Microbiology

Techniques

Comparison of sampling methods for profiling cervicovaginal microbiome in rhesus macaques. Schmidt BA. Journal of  Medical Primatology.

Qiita: rapid, web-enabled microbiome meta-analysis.Gonzalez A. Nature Methods

Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.Rotimi AM. BMC Bioinformatics

Animal Microbiome and Experiments

White spot syndrome virus (WSSV) infection impacts intestinal microbiota composition and function in Litopenaeus vannamei.Wang Jl; Fish and Shellfish Immunology

Dietary or supplemental fermentable fiber intake reduces the presence of Clostridium XI in mouse intestinal microbiota: The importance of higher fecal bacterial load and density.Zheng W. PLoS One

<i>Diplogastrellus</i> nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host.Ledón-Rettig CC. PNAS

The response of ruminal fermentation, epithelium-associated microbiota, and epithelial barrier function to severe feed restriction in pregnant ewes.Hu F. Journal of Animal Science

Rabbit Microbiota Changes Throughout the Intestinal Tract. Velasco-Galilea M. Frontiers in Microbiology

Antibiotic treatment of rat dams affects bacterial colonization and causes decreased weight gain in pups. Tulstrup MV. Communications Biology

Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages.Black EM. Microbiology Open

Effect of Different Disinfectants on Bacterial Aerosol Diversity in Poultry Houses.Jiang L. Frontiers in Microbiology

Effects of organic acid and medium chain fatty acid blends on the performance of sows and their piglets.  Lan R. Animal Science Journal

Microbial community composition and electricity generation in cattle manure slurry treatment using microbial fuel cells: effects of inoculum addition. Xie B. Environmental Science and Pollution Research

Plant, Soil, and Air Microbiome

Response of soil enzymes, functional bacterial groups, and microbial communities exposed to sudan I-IV. Teng Y. Ecotoxicology and Environmental Safety

Erratum: “Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification”.Salvetti E. Applied and Environmental Microbiology

Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado. de Araujo ASF. Communications Biology

Application of phosphate solubilizing bacteria in immobilization of Pb and Cd in soil.Yuan Z. Environmental Science and Pollution Research

Inland Waters and Marine Microbiome

Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities.Dittmann KK. Environmental Microbiology Reports

Novel T4 bacteriophages associated with black band disease in corals.Buerger P. Environmental Microbiology

Environmental conditions affect activity and associated microorganisms of marine sponges.Batista D. Marine Environmental Research

The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations.Vieira A. Applied Microbiology and Biotechnology

Antibiotics/Probiotics

Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes. Cairns J. Communications Biology

Metabolome/ Proteomics

Metaproteomics Study of the Gut Microbiome.Lai LA. Methods Molecular Biology: Functional Proteomics

COMMENTARY: Making the Case for Functional Proteomics. Perkins RC. Methods Molecular Biology: Functional Proteomics

REVIEW:Metabolome analysis for investigating host-gut microbiota interactions.Chen MX. Journal of Formosan Medical Association

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19 September, 2018

Today’s midweek digest includes a brilliant review on the occurrence of HGT within human holobiont and a¬†new approach to analysing microbiome data

General Microbiome

REVIEW: Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.Sitaraman R. Microbiome

Epidemiological aspects of healthcare-associated infections and microbial genomics.Mirande C. Europeans Journal of Clinical Microbiology and Infectious Diseases

Association between Cigarette Smoking Status and Composition of Gut Microbiota: Population-Based Cross-Sectional Study. Lee SH. Journal of Clinical Medicine

REVIEW: Proteomics and the microbiome: pitfalls and potential.Lin H. Expert Review of Proteomics

Biological films adhering to the oral soft tissues: structure, composition and potential impact on taste perception.Neyraud E. Journal of Texture Studies

Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing. Flaherty BR. Microbiome

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis.Jarett JK. Microbiome

The Extended Genotype: Microbially Mediated Olfactory Communication.Carthey AJR. Trends in Ecology and Evolution

Ceftriaxone administration disrupts intestinal homeostasis, mediating non-inflammatory proliferation and dissemination of commensal enterococci.Chakraborty R. Infection and Immunity

Gut Microbiome

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly.Martínez I. eLIFE

Human gut <i>Bacteroides</i> capture vitamin B<sub>12</sub> via cell surface-exposed lipoproteins.Wexler AG. eLIFE

Structural basis for the role of serine-rich repeat proteins from <i>Lactobacillus reuteri</i> in gut microbe-host interactions.Sequeira S. PNAS

Rapid and complete dehalogenation of halonitromethanes in simulated gastrointestinal tract and its influence on toxicity. Yin J. Chemosphere.

Diet: Cause or Consequence of the Microbial Profile of Cholelithiasis Disease?Gutiérrez-Díaz I. Nutrients

Immobilization stress-induced Escherichia coli causes anxiety by inducing NF-őļB activation through gut microbiota disturbance. Jang HM. Scientific Reports

Salmonella stimulates pro-inflammatory signalling through p21-activated kinases bypassing innate immune receptors.Sun H. Nature Microbiology

Lung Microbiome

Deciphering the Lung Microbiome: Implications for Lung Health and Disease.Johnson MM. Respiration

Plant and Soil Microbiome

Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico. Sánchez-Soto Jiménez MF. PeerJ.

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

Molecular characterization and detection of 16SrIII group phytoplasma associated with Huanglongbing symptoms.Wulff NAA. Phytopathology

Water Microbiome

Analysis of Bacterial Community Structure of Activated Sludge from Wastewater Treatment Plants in Winter. Xu S. BioMed Research International

Biological As(III) oxidation in biofilters by using native groundwater microorganisms.Crognale S. Science of the Total Environment

Animal Experiments and Microbiome

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate. Bredon M. Microbiome

The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome.Dranse HJ. PeerJ

Techniques

KERNEL-PENALIZED REGRESSION FOR ANALYSIS OF MICROBIOME DATA.Randolph TW. The Annals of Applied Statistics

August 27, 2018

Highlights: how microbes influence the system they inhabit, maternal microbial metabolism, gut microbiota in pancreatic disease and other metabolic disorders, core and staphylococcal microbiota in skin & nose of pigs, wheat head microbiome bacteria,  abundant & rare biospheres of hot springs, antibiotic degradation by microbes, virome.

General microbiome

Review:¬†Understanding how microbiomes influence the systems they inhabit¬†–¬†Ed K. Hall – Nature Microbiology

Male Bladder Microbiome Relates to Lower Urinary Tract Symptoms¬†–¬†Petar Bajic –¬†European Urology Focus

Pregnancy and early life

Is maternal microbial metabolism an early-life determinant of health?¬†–¬†Kymberleigh A. Romano – LabAnimal

Human oral microbiome

The oral microbiome in oral lichen planus during a one‚Äźyear randomized clinical trial¬†–¬†Camilla Kragelund – Oral Diseases

Human respiratory microbiome

Interaction between the microbiome and TP53 in human lung cancer¬†–¬†K.¬†Leigh¬†Greathouse – Genome Biology

Human gut microbiome

The Gut Microbiome in Pancreatic Disease¬†–¬†Venkata S. Akshintala –¬†Clinical Gastroenterology and Hepatology

FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid¬†–¬†Elliot S. Friedman – Gastroenterology

Review:¬†Role of gut microbiota in chronic low‚Äźgrade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies¬†–¬†I. C. L. van den Munckhof – Obesity Reviews

Bile acid homeostasis and intestinal dysbiosis in alcoholic hepatitis¬†–¬†Dragos Ciocan –¬†Alimentary Pharmacology & Therapeutics

Characterization and induction of prophages in human gut-associated Bifidobacterium hosts¬†–¬†Travis N. Mavrich – Scientific Reports

In Vitro Ecological Response of the Human Gut Microbiome to Bioactive Extracts from Edible Wild Mushrooms¬†–¬†Emanuel Vamanu – Molecules

Review:¬†The journey of gut microbiome ‚Äď An introduction and its influence on metabolic disorders –¬†Ankita¬†Chattopadhyay -Frontiers in Biology

Animal experiments 

Sulfated polysaccharide from sea cucumber modulates the gut microbiota and its metabolites in normal mice¬†–¬†Zhenjun¬†Zhu –¬†International Journal of Biological Macromolecules

Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota¬†–¬†Keisuke Nakashima – Nature Communications

Reduced particle size wheat bran is efficiently colonized by lactic acid producing community and reduces Enterobacteriaceae levels in the cecal microbiota of broilers –¬†Karen Vermeulen – Applied and Environmental Microbiology

A High Salt Diet Modulates the Gut Microbiota and Short Chain Fatty Acids Production in a Salt-Sensitive Hypertension Rat Model¬†–¬†Ariel Bier – Nutrients

Animal microbiome 

A detailed investigation of the porcine skin and nose microbiome using universal and Staphylococcus specific primers¬†–¬†Mikael Lenz Strube – Scientific Reports

Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions –¬†Daniel Crespo-Piazuelo – Scientific Reports

Cnidarian Interaction with Microbial Communities: From Aid to Animal‚Äôs Health to Rejection Responses¬†–¬†Loredana Stabili – Marine Drugs

Plant, root, and soil microbiome

Wheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation¬†–¬†Yun Chen – Nature Communications

Biodegradation of oxytetracycline and enrofloxacin by autochthonous microbial communities from estuarine sediments –¬†Malek¬†Harrabi –¬†Science of The Total Environment

Soil micro-food web interactions and rhizosphere priming effectSoil micro-food web interactions and rhizosphere priming effect¬†–¬†Xinchang¬†Kou – Plant and Soil

Burkholderia pseudomallei-absent soil bacterial community results in secondary metabolites that kill this pathogen¬†–¬†Chotima¬†Potisap – AMB Express

Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit¬†–¬†Jessica Wallace – PeerJ

Contrasting responses of the bacterial communities in ectomycorrhizal roots and rhizosphere soils to defoliation or winter hardening¬†–¬†Hironari¬†Izumi – Rhizosphere

Water and extremophile microbiome 

Abundant and rare microbial biospheres respond differently to environmental and spatial factors in Tibetan hot springs РYanmin Zhang РFrontiers in Microbiology

Built environment 

Review: Microbiology of the built environment РJack A Gilbert РNature Reviews

Application of hybrid anaerobic reactor: Treatment of increasing cyanide containing effluents and microbial composition identification¬†– Pragya Gupta –¬†Journal of Environmental Management

A little breath of fresh air into an anaerobic system: How microaeration facilitates anaerobic digestion process¬†–¬†Duc¬†Nguyen –¬†Biotechnology Advances

Managing microbial communities in membrane biofilm reactors¬†–¬†A.¬†Ontiveros-Valencia –¬†Applied Microbiology and Biotechnology

Phages and viruses

Preprint:¬†May the phage be with you? Prophage-like elements in the genomes of Soft Rot Pectobacteriaceae (Pectobacterium spp. and Dickeya spp.)¬†–¬†Robert Czajkowski – bioRxiv

Occurrence, integrity and functionality of AcaML1‚Äďlike viruses infecting extreme acidophiles of the Acidithiobacillus species complex¬†–¬†Paulo C.¬†Covarrubias – Research in Microbiology

Chapter:¬†Robust Analysis of Time Series in Virome Metagenomics¬†–¬†Jose¬†Manuel¬†Mart√≠ – The Human Virome

Chapter:¬†A Method for Isolation of the Virome from Plasma Samples¬†–¬†Pilar¬†Domingo-Calap – The Human Virome

Chapter:¬†Virome Sequencing of Stool Samples¬†–¬†Lenka¬†Kramn√° – The Human Virome

Chapter:¬†Protocol for Generating Infectious RNA Viromes from Complex Biological Samples¬†–¬†Sonia¬†Monteil-Bouchard – The Human Virome

Techniques

Review:¬†Transcriptome Sequencing Approaches to Elucidate Host‚ÄďMicrobe Interactions in Opportunistic Human Fungal Pathogens –¬†Hrant¬†Hovhannisyan –¬†Current Topics in Microbiology and Immunology¬†

Chapter:¬†Flow Cytometry and Direct Sequencing of Viruses¬†–¬†M√°ria¬†DŇĺunkov√° – The Human Virome

 

 

August 5, 2018

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 Р Amandeep Singh РNutrition 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 РCécile Angebault РPLoS 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

Article post

Microbiota depletion shifts colonocyte substrate utilization

In the fed state, glucose is the major fuel to most cell types in the body. In contrast, colonic epithelial cells or colonocytes utilize butyrate as their major energy source. Butyrate is one of the short chain fatty acids (SCFAs), a class of microbial metabolites produced by microbial fermentation of dietary fiber in gut. When the gut microbiota is depleted, such as in germ-free (GF) mice, butyrate levels along with other SCFAs decline prompting ‚Äústarved‚ÄĚ colonocytes to shift their substrate utilization to an alternative fuel, such as glucose.

Glucose undergo oxidative metabolism in cells to produce energy. In contrast, early ex vivo experiments studying substrate utilization in isolated colonocytes of rats using radioactive tracers revealed that about 80% of glucose is rather converted into lactate in colonocytes [1]. Later Donohoe et al., found that colonocytes from GF mice produce approx. 4 times higher lactate compared with conventionally raised mice through anaerobic glycolysis of glucose [2]. However, lactate production is not an energy rewarding process and yields only 2-4 ATP compared with 36 ATPs from oxidative phosphorylation of glucose. Thus, the authors concluded that despite the shift in substrate utilization, the colonocytes in the GF mice remain in energy insufficient state [2].

In the recent article published in Nature Communications by Zarrinpar et al. [3], where gut microbiota (and butyrate!) was depleted using multiple gavage of antibiotics over the course of 4 weeks. The authors found that cecum tissue uses glucose as an alternative fuel in the absence of butyrate, and that the expression levels of 8 out of 10 enzymes in glycolysis pathway were upregulated in cecum of antibiotic- compared with vehicle-treated mice. Finally, they speculate that due to shift in substrate utilization in cecum, gut becomes a glucose sink that could account for overall improvement in glucose metabolism in the antibiotic-treated mice [3].

Perhaps this speculation needs more careful investigation. It is true that colonocytes use butyrate as their primary fuel; however, butyrate is not synthesized in isolation. Gut microbiota produces SCFAs that include acetate, propionate and butyrate. It has been shown that colonocytes prefer other SCFA such as acetate over glucose [4] probably because anaerobic glycolysis of glucose does not yield enough energy. In the article by Zarrinpar et al., there was a trend towards reduction of acetate in antibiotic- compared with vehicle-treated mice, but it was not depleted to the same level as butyrate [3]. Secondly, shift in colonocyte substrate utilization from butyrate to glucose is also observed in inflammatory bowel disease and DSS colitis model. This is indicated to be due to alteration in butyrate uptake and thus colonocytes utilize glucose leading to high amount of lactate accumulation in cells [5]. However, patients with IBS are more prone to develop glucose intolerance than the healthy people.

Studying substrate utilization in cecum/colonocytes is complex. It is true that the isolated colonocytes do not reflect the in vivo scenario. However, transcriptomic data (showing increased expression of glycolytic enzymes in intestinal tissue of antibiotic-treated mice) probably needs to be backed with enzyme activity measurements and tracer studies to  understand its impact on overall metabolism.

1. Ardawi, M.S. and E.A. Newsholme, Fuel utilization in colonocytes of the rat. Biochem J, 1985. 231(3): p. 713-9.

2. Donohoe, D.R., et al., Microbial regulation of glucose metabolism and cell-cycle progression in mammalian colonocytes. PLoS One, 2012. 7(9): p. e46589.

3. Zarrinpar, A., et al., Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun, 2018. 9(1): p. 2872.

4. Clausen, M.R. and P.B. Mortensen, Kinetic studies on the metabolism of short-chain fatty acids and glucose by isolated rat colonocytes. Gastroenterology, 1994. 106(2): p. 423-32.

5. Thibault, R., et al., Butyrate utilization by the colonic mucosa in inflammatory bowel diseases: a transport deficiency. Inflamm Bowel Dis, 2010. 16(4): p. 684-95.

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.

 

 

June 22, 2018

Have a happy weekend! Today in Microbiome Digest: reviews on microbiome immunity and type 1 diabetes, ¬†metatranscriptome analysis of vaginal microbiome, Differences in gut microbiota associated with age, sex, and stool consistency, microbes in the news, and more…

Events and jobs

Scientist – Genomics and Microbiome – Madison, WI

Bioinformatics Scientific Programmer – Quadram Institute Bioscience

General microbiome

Review: Communication Between the Microbiota and Mammalian Immunity РKyla S. Ost РAnnual Review of Microbiology

Host genotype-specific microbiota do not influence the susceptibility of¬†D.¬†magna¬†to a bacterial pathogen – Marilou P. Sison-Mangus ‚Äď Scientific Reports

Pregnancy and early life

Book chapter: Implantation Failure 1: Intrauterine Circumstances and Embryo‚ÄďEndometrium Synchrony at Implantation – Keiji¬†Kuroda – Treatment Strategy for Unexplained Infertility and Recurrent Miscarriage

Special Issue: Microbiome in normal and pathological pregnancies: A literature overview – Carla R. Taddei ‚Äď American Journal of Reproductive Immunology

Multi-site human microbiome

Bacterial invasion of dentinal tubules from the external root surface with and without an intact cemental layer- a confocal laser scanning microscopic study РJovita D’souza РAdvances in Tissue Engineering and Regenerative Medicine

Human respiratory microbiome

Review: Drug Resistance and Gene Transfer Mechanisms in Respiratory/Oral Bacteria – Jiang S – Journal of Dental Research

Ecology and diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study Р Abigail L. Coughtrie РJournal of Medical Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood ‚Äď Scientific Reports

Human vaginal microbiome

Review: Pharmacology of Antiretrovirals in the Female Genital Track for HIV Prevention – Melanie R. Nicol ‚Äď The Journal of Clinical Pharmacology

Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis – Zhi-Luo Deng ‚Äď mSphere¬†

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review РZheng P РDiabetes/Metabolism Research and Reviews

A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile РThanissery R РFrontiers in Microbiology

Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects РTomohisa Takagi РJournal of Gastroenterology

Dietary Supplementation with a Magnesium-Rich Marine Mineral Blend Enhances the Diversity of Gastrointestinal Microbiota – Erin K. Crowley ‚Äď Marine Drugs

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms – Brandon Brooks ‚Äď Microbiome

Review: Potential Role of the Gut Microbiome in ALS: A Systematic Review – Michelle L. Wright – Biological Research for Nursing

Animal experiments

Lack of liver steatosis in germ-free mice following hypercaloric diets РStephan C. Bischoff РEuropean Journal of Nutrition

 Plant, root, and soil microbiome

Exploring Elicitors of the Beneficial Rhizobacterium Bacillus amyloliquefaciens SQR9 to Induce Plant Systemic Resistance and Their Interactions With Plant Signaling Pathways ‚Äď Gengwei Wu – Molecular Plant-Microbe Interactions

Correlation and Distribution of Xenobiotics Genes and Metabolic Activities with Level of Total Petroleum Hydrocarbon in Soil, Sediment and Estuary Water in the Niger Delta Region of Nigeria U. O. Edet – Asian Journal of Biotechnology and Genetic Engineering

Review: Status and future of disease protection and grape berry quality alteration by microorganisms in viticulture – Misa Otoguro ‚Äď Letters in Applied Microbiology

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

Water and extremophile microbiome

Mini-Review: Future direction in marine bacterial agarases for industrial applications -Saeid Tamadoni Jahromi РApplied Microbiology and Biotechnology

Prokaryotic assemblages in the maritime Antarctic Lake Limnopolar (Byers Peninsula, South Shetland Islands) РM. Papale РExtremophiles

Taxonomy, phylogeny and ecology of cultivable fungi present in seawater gradients across the Northern Antarctica Peninsula РVívian N. Gonçalves РExtremophiles 

A strong link between marine microbial community composition and function challenges the idea of functional redundancy – Pierre E. Galand – The ISME Journal

Probiotics / prebiotics

Gut Microbiota, Probiotics, and Sport: From Clinical Evidence to Agonistic Performance – Marco Pane – Journal of Clinical Gastroenterology

 Microbes in the news

‘Green’-feed: Industrial microbes could feed cattle, pigs, chicken

SMU researchers hope microbes will lead them to strike oil offshore

Scientists Reveal How Gut Microbes ‘Recover’ After Antibiotic Treatment

Celebrate your gut microbiota on the first World Microbiome day!

 Microbes on the market (news about biotech companies)

Human Microbiome Market – Global Industry Analysis, Size, Share, Growth, Trends, and Forecast 2018 – 2026

MaaT Pharma and Lutech Sign Licensing Agreement on Microbiome Therapy for Graft-vs-Host Disease

 

Ashok’s non-microbiology picks

The Rheumatoid Arthritis-Associated Citrullinome – Ronak Tilvawala ‚Äď Cell Chemical Biology

Inflammation-Induced, STING-Dependent Autophagy Restricts Zika Virus Infection in the¬†Drosophila¬†Brain – Yuan Liu ‚Äď Cell Host & Microbe

Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells – Patrick Fernandes Rodrigues – Nature Immunology

A synaptic threshold mechanism for computing escape decisions – Dominic A. Evans ‚Äď Nature