January 14, 2019

Today’s digest is about the CRISPR tools for diverse bacteria, urinary microbiome associated with bladder cancer and OMeta, a data-driven metadata tracking system. Happy reading!

Gut microbiome

*Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi – Jason M. Peters – Nature Microbiology

Urinary microbiome

*Review: The Urinary Microbiome: Implications in Bladder Cancer Pathogenesis and Therapeutics – Petar Bajic – Urology

Animal experiments

High-fat diet causes psychiatric disorders in mice by increasing Proteobacteria population – Mi-Young Jeong – Neuroscience Letters

Animal microbiome

Canine endometrial and vaginal microbiomes reveal distinct and complex ecosystems – Candace C. Lyman – PlosOne

Probiotic characterization of Lactobacillus isolates from canine faeces – Maria Magdalena Coman – Journal of Applied Microbiology

Water microbiome

Deciphering of microbial community and antibiotic resistance genes in activated sludge reactors under high selective pressure of different antibiotics – Renxin Zhao – Water Research

Desiccation events change the microbial response to gradients of wastewater effluent pollution – Ferran Romeroa – Water Research

Characteristics of pipe corrosion scales in untreated water distribution system and effect on water quality in Peshawar, Pakistan – Dilawar Farhan Shams – Environmental Science and Pollution Research

Plant/root/soil microbiome

Microbial phyto-power systems – A sustainable integration of phytoremediation and microbial fuel cells – Beenish Saba – Bioelectrochemistry

A Plant‐Growth Promoting Bacterium Alters the Microbial Community of Continuous Cropping Poplar Trees Rhizosphere – Junkang Sui – Journal of Applied Microbiology

Bioinformatics

*OMeta: an ontology-based, data-driven metadata tracking system – Indresh Singh – BMC Bioinformatics

January 1, 2019

Posted on January 1, 2019 by xinhuang7

Happy New Year! 2019 comes with a short Digest featuring a review on metabolic regulation by gut microbiota and a high throughput yeast two-hybrid screening method. May 2019 bring much success and happiness.

General microbiology

Probabilistic modeling of microbial networks for integrating partial quantitative knowledge within the nitrogen cycle – Damien Eveillard et al. – Frontiers in Microbiology

Methods to Watch: Microbial interactions – Lei Tang – Nature Methods

Human gut microbiome

Dietary quality of predominantly traditional diets is associated with blood glucose profiles, but not with total fecal Bifidobacterium in Indonesian women – Shiela Stefani et al. – PLoS One

** Review: Gut microbiota as important modulator of metabolism in health and disease – Xiang-qian Wang et al. – Royal Society of Chemistry Advances

Review: Colonization and probiotic function of Bifidobacterium longum – Chengcheng Zhang et al. – Journal of Functional Foods

Food microbiome

Microbial communities and volatile metabolites in different traditional fermentation starters used for Hong Qu glutinous rice wine – Zi-Rui Huang et al. – Food Research International

Plant, root and soil microbiome

Soil parameters drive the diversity of Citrus sinensis rhizosphere microbiota which exhibits a potential in plant drought stress alleviation – Marwa Cherni et al. – Applied Soil Ecology

Revealing microbial processes and nutrient limitation in soil through ecoenzymatic stoichiometry and glomalin-related soil proteins in a retreating glacier forefield – Yonglei Jiang et al. – Geoderma

Water and extremophile microbiome

Co-occurrence patterns of the microbial community in polycyclic aromatic hydrocarbon-contaminated riverine sediments – Zaisheng Yan et al. – Journal of Hazardous Materials

Addition of algicidal bacterium CZBC1 and molasses to inhibit cyanobacteria and improve microbial communities, water quality and shrimp performance in culture systems – Wujie Xu et al. – Aquaculture

Sludge anaerobic digestion with high concentrations of tetracyclines and sulfonamides: dynamics of microbial communities and change of antibiotic resistance genes – Yang Bai et al. – Bioresource Technology

Temperature dependence of denitrification microbial communities and functional genes in an expanded granular sludge bed reactor treating nitrate-rich wastewater – Runhua Liao et al. – Royal Society of Chemistry Advances

Built environment microbiome

Bacillus species at the Canberra Airport: A comparison of real-time polymerase chain reaction and massively parallel sequencing for identification – M.E. Gahan et al. – Forensic Science International

Technology

** A user-friendly platform for yeast two-hybrid library screening using next generation sequencing – Marie-Laure Erffelinck & Bianca Ribeiro et al. – PLoS One

December 30, 2018

Posted on December 30, 2018 by ojasvi

In the midst of the festive season have a fiesta with the recent articles on Microbiome. Todays MicroBiome Digest covers the Techniques and Treatments, Drugs, Immunostimulatory Diet and Nutrition, Multivariate Count Data Model, Antimicrobials, Pre/Pro-biotcs, Host-Microbe Interactions, Genes, Genomics and Pathways of Microbiota, Infant Microbiome, Animal Models, Animal Microbiome, Microbial Ecology of plant and soil. Happy Reading!!!

TECHNIQUES & TREATMENTS:

LEMMI: A Live Evaluation of Computational Methods for Metagenome Investigation – Mathieu Seppey – bioRxiv

Single-cell virus sequencing of influenza infections that trigger innate immunity – Alistair B Russell – bioRxiv

METHODS TO IMPROVE INDUCTION OF IGG AND IGA ANTIBODIES BY VACCINES – Boyaka, Prosper -United States Patent Application 20180360953 -PATENT

Are the Statins promising antifungal agents against invasive candidiasis? – William GustavoLima -Biomedicine & Pharmacotherapy

Bayesian variable selection for multivariate zero-inflated models: Application to microbiome count data – Lee KH – Biostatistics

Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing – Mu DS – Microbiome

Prognostic Impact of Fusobacterium nucleatum Depends on Combined Tumor Location and Microsatellite Instability Status in Stage II/III Colorectal Cancers Treated with Adjuvant Chemotherapy – Oh HJ – J Pathol Transl Med.

Loss of Gut Microbiota Alters Immune System Composition and Cripples Post-Infarction Cardiac Repair – Tang TW – Circulation

DRUG, DIET and NUTRITION:

Review article: implementation of a diet low in FODMAPs for patients with irritable bowel syndrome-directions for future research – Mitchell Hrticle – Aliment Pharmacol Ther.

Compound polysaccharides ameliorate experimental colitis by modulating gut microbiota composition and function – Cai Y – J Gastroenterol Hepatol.

Rifaximin Altered Gut Microbiota Components Associated with Liver/Neuropsychological Functions in Patients with Hepatic Encephalopathy: An Exploratory Data Analysis of a Phase II/III Clinical Trials – Kawaguchi T – Hepatol Res.

Inulin ameliorates alcoholic liver disease via suppressing LPS-TLR4-Mψ axis and modulating gut microbiota in mice – Yang X – Alcohol Clin Exp Res.

Effect of Resistant Starch on the Gut Microbiota and Its Metabolites in Patients with Coronary Artery Disease – Yoshida N – J Atheroscler Thromb.

Late gestation diet supplementation of resin acid-enriched composition increases sow colostrum immunoglobulin G content, piglet colostrum intake and improve sow gut microbiota – Hasan S – Animal

PRE/PRO- BIOTICS and ANTIMICROBIAL:

The human skin microbiota is a rich source of bacteriocin producing staphylococci which kill human pathogens – O’Sullivan JN – FEMS Microbiol Ecol.

Comparative immunostimulatory effect of probiotics and prebiotics in Channa punctatus against Aphanomyces invadans – Devi G – Fish Shellfish Immunol

GENES, GENOMICS & PATHWAYS:

Detection of a novel mutation G511T in the 530 loop in 16S rRNA in multi drugs resistant Mycobacterium tuberculosis isolated from Sudanese patients – Yousif Mohammed Alfatih – bioRxiv

Review: Interactions Between Autophagy and the Unfolded Protein Response: Implications for Inflammatory Bowel Disease – Hooper KM – Inflamm Bowel Dis.

In vitro and in vivo characterization of Clostridium scindens bile acid transformations – Marion S- Gut Microbes

Bioinformatic, phylogenetic, and chemical analysis of the UV-absorbing compounds scytonemin and mycosporine-like amino acids from the microbial mat communities of Shark Bay, Australia – D’Agostino PM – Environ Microbiol

Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses – Tyakht AV – BMC Genomics

Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan – Sekizuka T – mSphere

HOST-MICROBE INTERACTION:

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles – Antoine P Pagé -bioRxiv

Bacterial secretion of histamine within the gut influences immune responses within the lung – Barcik W – Allergy

GUT MICROBIOME:

Extensive Transmission of Microbes along the Gastrointestinal Tract – Thomas SB Schmidt – bioRxiv

VAGINAL MICROBIOME:

Human β-defensin-2 as a biochemical indicator of vaginal environment in pregnant women – Hideko Kotani – Hypertension Research In Pregnancy

PREGNANCY AND EARLY LIFE:

Physiology of Stress and Use of Skin-to-Skin Care as a Stress-Reducing Intervention in the NICU – Britt Frisk Pados – Nursing for Women’s Health

Longitudinal analysis of infant stool bacteria communities before and after acute febrile malaria and artemether/lumefantrine treatment – Mandal RK – J Infect Dis.

Haemophilus-dominant nasopharyngeal microbiota is associated with delayed clearance of respiratory syncytial virus in infants hospitalized for bronchiolitis – Mansbach JM – J Infect Dis

ANIMAL MODEL EXPERIMENTS:

Dietary nucleotides can directly stimulate the immunity of zebrafish independent of the intestinal microbiota – Guo X – Fish Shellfish Immunol.

Antimicrobial assessment of phage therapy using a porcine model of biofilm infection – Milho C – Int J Pharm

ANIMAL MICROBIOME:

Effect of different levels of tryptophan on productive performance, egg quality, blood biochemistry, and caecal microbiota of hens housed in enriched colony cages under commercial stocking density – Khattak F -Poult Sci.

Exogenous carbohydrases added to a starter diet reduced markers of systemic immune activation and decreased Lactobacillus in weaned pigs – Li Q – J Anim Sci.

Gut microbiota dynamics and functionality in Reticulitermes grassei after a 7-day dietary shift and ciprofloxacin treatment – Berlanga M – PLoS One

MICROBIAL ECOLOGY:

Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia – Yasir M – OMICS

Rhizosphere microorganisms can influence the timing of plant flowering – Lut T – Microbiome

December 26, 2018

Posted on December 26, 2018 by Tulika Arora

Holidays, Happiness and some updates on the microbiome!
Today’s short digest covers functions of different Lactobacillus strains; how weaning stress affects the gut microbiome and association of bacterial metabolite TMAO with Alzheimer’s disease.

General microbiome

Review: Antibiotics and the nervous system: More than just the microbes? – Kevin Champagne-Jorgensen – Brain, Behavior, and Immunity

Human gut microbiome

The gut microbiota-derived metabolite trimethylamine N-oxide is elevated in Alzheimer’s disease – Nicholas M. Vogt – Alzheimer’s Research & Therapy

A novel probiotic, Lactobacillus johnsonii 456, resists acid and can persist in the human gut beyond the initial ingestion period – Michael J. Davoren – Gut Microbes

Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa – Mun Fai Loke – PlosOne

Human oral/respiratory microbiome

The Salivary Microbiome: Analysis of by Pyrosequencing and the Relationship with Helicobacter pylori Infection – Yingjie Ji – bioRxiv

Differences in the lower airway microbiota of infants with and without cystic fibrosis – Katherine B. Frayman – Journal of Cystic Fibrosis

Animal experiments

A Diet-Sensitive Commensal Lactobacillus Strain Mediates TLR7-Dependent Systemic Autoimmunity – Daniel F. Zegarra-Ruiz – Cell Host and Microbe

The gut microbiome is required for full protection against acute arsenic toxicity in mouse models – Michael Coryell – Nature Communications

Weaning Stress Perturbs Gut Microbiome and Its Metabolic Profile in Piglets – Yuan Li – Scientific Reports

Plant root soil microbiome

The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory – Charley J. Hubbard – Molecular Ecology

Enrichment of Verrucomicrobia, Actinobacteria and Burkholderiales drives selection of bacterial community from soil by maize roots in a traditional milpa agroecosystem – Eneas Aguirre-von-Wobeser – PlosOne

Non-microbiology picks

Friend and foe: β-cell Ca2+ signaling and the development of diabetes – Paul V. Sabatini – Molecular Metabolism

December 22, 2018

Posted on December 22, 2018 by JP Cardenas

Have a good weekend! Today, we have several studies about different compounds with beneficial effects in human and animal models.

General Microbiome

Review: Functions of the Microbiota for the Physiology of Animal Metaorganisms – Esser D – Journal of Innate Immunology

Feasibility of shotgun metagenomics to assess microbial ecology of pediatric tracheostomy tubes – James C. Wang – The Laryngoscope

Review: Microbiota and Food Allergy – Shang-An Shu – Clinical Reviews in Allergy & Immunology

Review: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity – Amy Proal – Frontiers in Pediatrics

Alterations in the Gut Microbiota and Metabolite Profiles of Thyroid Carcinoma Patients – Jing Feng – International Journal of Cancer

Review: Zero tolerance! A perspective on monogenic disorders with defective regulatory T cells and IBD-like disease – Ussama M. Abdel‐Motal – Immunological Reviews

Review shows that donor milk does not promote the growth and development of preterm infants as well as maternal milk – Anna‐Lena Hård – Acta Paedriatica

An Investigation Into Physical Frailty as a Link Between the Gut Microbiome and Cognitive Health – Serena Verdi – Frontiers in Aging Neuroscience

Review: Microorganisms’ Footprint in Neurodegenerative Diseases – Mona Dehhaghi – Frontiers in Cellular Neuroscience

Impact of dietary fiber supplementation on modulating microbiota-host-metabolic axes in obesity – Shyamchand Mayengbam – The Journal of Nutritional Biochemistry

Gut microbiome-based secondary metabolite biosynthetic gene clusters detection in Parkinson’s disease – Shengqin Wang – Neuroscience Letters

Different host factors are associated with patterns in bacterial and fungal gut microbiota in Slovenian healthy cohort – Aleksander Mahnic – PLOS One

Childhood Asthma: Advances Using Machine Learning and Mechanistic Studies – Sejal Saglani – American Journal of Respiratory and Critical Care Medicine

Assessing the Influence of Dietary History on Gut Microbiota – Bo Yang – Current Microbiology

Review: The Role of Microbiome in Insomnia, Circadian Disturbance and Depression – Yuanyuan Li – Frontiers in Psychiatry

Gut microbiota and overweight in 3-year old children – Anne M. Karvonen – International Journal of Obesity

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome – Arnau Vich Vila – Science Translational Medicine

Hydrogen cross-feeders of the human gastrointestinal tract – Nick W. Smith – Gut Microbes

A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet – Chiharu Ishii – International Journal of Molecular Sciences

Built Environment

Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system – Laura E. Williams – PeerJ

Food Microbiome

Microbiota composition of dadih – a traditional fermented buffalo milk of West Sumatra – Koen Venema – Letters in Applied Microbiology

Beneficial Microbes and Compounds

Book Chapter: Use of Probiotics to Prevent Celiac Disease and IBD in Pediatrics – Gloria Serena – Part of the Advances in Experimental Medicine and Biology book series

Review: Dietary compounds and traditional Chinese medicine ameliorate type 2 diabetes by modulating gut microbiota – Qixing Nie – Critical Reviews in Food Science and Nutrition

Antidiabetic Potential of Green Seaweed Enteromorpha prolifera Flavonoids Regulating Insulin Signaling Pathway and Gut Microbiota in Type 2 Diabetic Mice – Xin Yan – Journal Of Food Science

Effects of bifidobacteria-produced exopolysaccharides on human gut microbiota in vitro – Guiyang Liu – Applied Microbiology and Biotechnology

Dietary geraniol ameliorates intestinal dysbiosis and relieves symptoms in irritable bowel syndrome patients: a pilot study – Fernando Rizzello – BMC Complementary and Alternative Medicine

Resveratrol-Induced White Adipose Tissue Browning in Obese Mice by Remodeling Fecal Microbiota – Weiyao Liao – Molecules

DHA-phospholipids (DHA-PL) and EPA-phospholipids (EPA-PL) prevent intestinal dysfunction induced by chronic stress – Wanxiu Cao – Food and Function

Chlorophyllin Modulates Gut Microbiota and Inhibits Intestinal Inflammation to Ameliorate Hepatic Fibrosis in Mice – Han Zheng – Frontiers in Physiology

Modulation of Gut Microbiota by Lonicera caerulea L. Berry Polyphenols in a Mouse Model of Fatty Liver Induced by High Fat Diet – Shusong Wu – Molecules

Pathogen Research

Peptide Ligands of AmiA, AliA, and AliB Proteins Determine Pneumococcal Phenotype – Fauzy Nasher – Frontiers in Microbiology

Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification – Matthew T. Sorbara – Journal of Experimental Medicine

Environmental Microbiome

Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations – Klervi Crenn – Frontiers in Microbiology

Plant Microbiome

Minireview: Plant health: feedback effect of root exudates-rhizobiome interactions – Oluwaseyi Samuel Olanrewaju – Applied Microbiology and Biotechnology

Techniques

A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes, and pure cultures – C. E. Thorn – Molecular Ecology Resources

More Microbes

An Update on the Evolution of Glucosyltransferase (Gtf) Genes in Streptococcus – Rong-Rong Xu – Frontiers in Microbiology

Repeated Evolutionary Transitions of Flavobacteria from Marine to Non-Marine Habitats – Hao Zhang – Environmental Microbiology

Genome-Guided Identification of Organohalide-Respiring Deltaproteobacteria from the Marine Environment – Jie Liu – mBio

December 21, 2018

Posted on December 20, 2018 by Svetlana Ugarcina Perovic

Today’s digest is about the shortcomings of the midstream urine test for urinary tract infection, contacts between phages and bacterial hosts, and contamination in marker-gene and metagenomic sequencing. There is a very interesting podcast on “Seeing double” in scientific papers. Happy reading/listening!

Urinary microbiome

Cross-over data supporting long-term antibiotic treatment in patients with painful lower urinary tract symptoms, pyuria and negative urinalysis – Sheela Swamy – International Urogynecology Journal

*Reassessment of routine midstream culture in diagnosis of urinary tract infection – Sanchutha Sathiananthamoorthya – Journal of Clinical Microbiology

Gut microbiome

Drivers of human gut microbial community assembly: Coadaptation, determinism and stochasticity – Kaitlyn Oliphan – BioRxiv

Animal experiments

*Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay – Martial Marbouty – Science Advances

Antidepressant treatment modulates the gut microbiome and metabolome during pregnancy and lactation in rats with a depressive-like phenotype – Anouschka S Ramsteijn – BioRxiv

General Anesthesia Alters the Diversity and Composition of the Intestinal Microbiota in Mice – Mara A. Serbanescu – Anesthesia & Analgesia

Water microbiome

Bacterial community activity and dynamics in the biofilm of an experimental hybrid wetland system treating greywater – Marika Truu – Environmental Science and Pollution Research

Plant/root/soil microbiome

Introducing THOR, a model microbiome for genetic dissection of community behavior – Gabriel L. Lozano – BioRxiv

Bacterial analogs of plant piperidine alkaloids mediate microbial interactions in a rhizosphere model system – Gabriel L. Lozano – BioRxiv

Bioinformatics

*Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data – Nicole M. Davis – Microbiome

Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences – Kirill Kryukov – BioRxiv

Podcast

*Seeing double [Elisabeth Bik speaks about the problematic images in scientific papers, the state of microbiome research, and making the jump from academia to industry] – Dan Quintana and James Heathers – Everything Hertz.

December 20, 2018

Posted on December 20, 2018 by Tulika Arora

In the wait of Christmas weekend and holidays, some quick reading for updates in microbiome field. Today’s digest include articles on improving metagenomic data analysis and integrating different -omics datasets; review article on potential of microbiome to address antimicrobial resistance and meta-analysis on benefits of probiotic supplements in kidney disease.

General microbiome

Microbiome as a tool and a target in the effort to address antimicrobial resistance – David A. Relman – PNAS

Gut microbiota and health: connecting actors across the metabolic system – F. Fava – Proceedings of the Nutrition Society

Dietary sugar silences a colonization factor in a mammalian gut symbiont – Guy E. Townsend II – PNAS

Human gut microbiome

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life – Tommi Vatanen – Nature Microbiology

Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota – Bálint Kintses – Nature Microbiology

Fecal Microbiota Transplantation for the Critically Ill Patient – Berkeley N. Limketkai – Nutrition in Clinical Practice

Effects of probiotic supplements on the progression of chronic kidney disease: a meta‐analysis – Sibei Tao – Nephrology

Signatures within the esophageal microbiome are associated with host genetics, age, and disease – Nandan P. Deshpande – Microbiome

Human oral microbiome

Oral microbiomes in children with asthma and dental caries – Sergey V. Cherkasov – Oral Diseases

Animal experiments

Microbial fermentation of flaxseed fibers modulates the transcriptome of GPR41-expressing enteroendocrine cells and protects mice against diet-induced obesity – Tulika Arora – Americal Journal of Physiology Endocrinology and Metabolism

Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome – Xiaoyun Wang – Cell Research

Antidepressant treatment modulates the gut microbiome and metabolome during pregnancy and lactation in rats with a depressive-like phenotype – Anouschka S. Ramsteijn – BioRxiv

Association of gut microbiota composition and function with a senescence-accelerated mouse model of Alzheimer’s Disease using 16S rRNA gene and metagenomic sequencing analysis – Weijun Peng – Aging

Prebiotics and synbiotics – in ovo delivery for improved lifespan condition in chicken – M. Siwek – BMC Veterinary Research

The response of colonic mucosa-associated microbiota composition, mucosal immune homeostasis, and barrier function to early-life galactooligosaccharides intervention in suckling piglets – Jue Wang – Journal of Agricultural and Food Chemistry

Techniques

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis – Michael H. Schwartz – Nature Communications

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data – Nicole M. Davis – Microbiome

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy – Mohammad Sajjad Ghaemi – Bioinformatics

Introducing THOR, a model microbiome for genetic dissection of community behavior – Gabriel L. Lozano – BioRxiv

Microbes in the news

Prebiotics Benefit the Gut Microbiome of Both Children and Adults – Market watch

Non-microbiology picks

Technologies to address antimicrobial resistance – Stephen J. Baker – PNAS

December 19, 2018

Posted on December 19, 2018 by Anitha Isaiah

Toady’s digest features research that gives insight on the formation of lower respiratory tract microbiota in infants and the differential role of TL1A in acute and chronic colitis.

General microbiome

Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease – Steven A. Cowman – PLOS ONE

Pregnancy and early life

*Early-Life Formation of the Microbial and Immunological Environment of the Human Airways – CélinePattaroni – Cell Host & Microbe

Human reproductive microbiome

Review: Uterine microbiome—low biomass and high expectations – Iolanda Garcia-Grau – Biology of Reproduction

Human respiratory microbiome

Review: Microbiome and disease in the upper airway – Jivianne T. Lee – Current Opinion in Allergy and Clinical Immunology

Human gut microbiome

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

Retrospective analysis of long-term gastrointestinal symptoms after Clostridium difficile infection in a nonelderly cohort – Tamar F. Barlam – PLOS ONE

Review: Gut microbiota: a potential manipulator for host adipose tissue and energy metabolism – Bohan Rong – The Journal of Nutritional Biochemistry

Animal experiments

*Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis – Jim G.Castellanos – Immunity

LC–MS-Based Metabolomics and Lipidomics Study of High-Density-Lipoprotein-Modulated Glucose Metabolism with an apoA-I Knockout Mouse Model – Jia Liu – Journal of Proteome Research

TLR4 deficiency reduces pulmonary resistance to Streptococcus pneumoniae in gut microbiota-disrupted mice – Hongyan Wang – PLOS ONE

Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats – Deliang Liu – Biomedicine & Pharmacotherapy

Animal microbiome

Floral and Foliar Source Affect the Bee Nest Microbial Community – Jason A. Rothman – Microbial Ecology

Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus – Matthew Fuirst – PLOS ONE

Disruption of the microbiota affects physiological and evolutionary aspects of insecticide resistance in the German cockroach, an important urban pest – Jose E. Pietri _ PLOS ONE

The composition and structure of the intestinal microflora of Anguilla marmorata at different growth rates: a deep sequencing study – Mao Lin – Journal of Applied Microbiology

Review: Composition and functional roles of the gut microbiota in mosquitoes – Michael R. Strand – Current Opinion in Insect Science

Review: Transcriptomic analyses uncover emerging roles of mucins, lysosome/secretory addressing and detoxification pathways in insect midguts – Walter R. Terra – Current Opinion in Insect Science

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals – Amanda C. Perofsky – The ISME Journal

Plant, root, and soil microbiome

Dead or alive; or does it really matter? Level of congruency between trophic modes in total and active fungal communities in High Arctic soil – Magdalena Wutkowska – Frontiers in Microbiology

Water and extremophile microbiome

Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities – Alberto Scoma- The ISME Journal

Evidence of selective pressure in whale fall microbiome proteins and its potential application to industry – Robert Cardoso deFreitas – Marine Genomics

AgNPs change microbial community structures of wastewater – Yuting Guo – Frontiers in Microbiology

Performance and microbial community of an electric biological integration reactor (EBIR) for treatment of wastewater containing ibuprofen – Yan Feng – Bioresource Technology

Food microbiology

Spoilage microbial community profiling by 16S rRNA amplicon sequencing of modified atmosphere packaged live mussels at cold storage temperature – Olumide A.Odeyemi – Food Research International

Genomic resolution of bacterial populations in saccharin and cyclamate degradation – YuDeng – Science of The Total Environment

Phages and viruses

Nanopore-based detection and characterization of yam viruses – Denis Filloux – Scientific Reports

Metabolomics

Active Acupoints Differ from Inactive Acupoints in Modulating Key Plasmatic Metabolites of Hypertension: A Targeted Metabolomics Study – Mingxiao Yang – Scientific Reports

Techniques

Review: Quantifying microbial chatter: scanning electrochemical microscopy as a tool to study interactions in biofilms – Sophie E. Darch – Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences

Metabolic Fingerprinting of Bacteria Exposed to Nanomaterials, Using Online Databases, NMR, and High-Resolution Mass Spectrometry – Theodoros G. Chatzimitakos – Nanotoxicity

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Science, publishing, and career

Commentary : Communicating health risks in science publications: time for everyone to take responsibility – Alexandra L. J. Freeman – BMC Medicine

Could a double blind peer review process reduce gender bias?

Preprint: The Case For and Against Double-blind Reviews – Amelia R – bioRxiv

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: General Microbiome

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