November 16, 2018

Happy Friday! Today’s digest includes the effects of chewing gum on the oral microbiome, the gill microbiome of mangrove shipworms, and the rumen microbiome of dairy cows. Enjoy!

Human oral microbiome

Effects of xylitol-containing chewing gum on the oral microbiota – Takeuchi – Journal of Oral Science

Human gut microbiome

Gut microbiome transition across a lifestyle gradient in Himalaya – Jha – PLoS Biology

Fecal chromogranins and secretogranins are linked to the fecal and mucosal intestinal bacterial composition of IBS patients and healthy subjects – Sundin – Scientific Reports

Animal experiments

Specific Members of the Gut Microbiota are Reliable Biomarkers of Irradiation Intensity and Lethality in Large Animal Models of Human Health – Carbonero – Radiation Research

Gut microbiota development in mice is affected by hydrogen peroxide produced from amino acid metabolism during lactation – Shigeno – FASEB Journal

Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells – Bodogai – Science Translational Medicine

Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice – Kaliannan – Microbiome

Effects of Intraoperative Vagal Nerve Stimulation on the Gastrointestinal Microbiome in a Mouse Model of Amyotrophic Lateral Sclerosis – Haney – Comparative Medicine

Animal microbiome

Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale – Wynants – Microbial Ecology

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei – Brito – PLoS One

Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows – Tong – PLoS One

Plant, root, and soil microbiome

Rootstocks shape the rhizobiome: Rhizosphere and endosphere bacterial communities in the grafted tomato system – Poudel – Applied and Environmental Microbiology

Water and extremophile microbiome

Aquatic ecotoxicity of an antidepressant, sertraline hydrochloride, on microbial communities – Yang – Science of The Total Environment

Probing the ecological and evolutionary history of a thermophilic cyanobacterial population via statistical properties of its microdiversity – Rosen – PLoS One

Built environment

Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis – Zhang – AMB Express

Analysis of bacteria stress responses to contaminants derived from shale energy extraction – Santos – Environmental Science: Processes & Impacts

Probiotics/prebiotics

Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial – Plummer – BMC Microbiology

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November 13, 2018

Today’s Digest features several soil and environmental microbiome papers, including the effect of fire on soil ecosystems, insights into the freshwater microbiome associated with the world’s largest mining disaster, applications of soils in forensics, and chemical leaching from LCD screens due to synergistic bacteria. Plus, check out some animal work in marine invertebrates (Sea stars and Ascidians) as well as minks, flying squirrels, and bees!

Pregnancy and early life
The profile of human milk metabolome, cytokines and antibodies in inflammatory bowel diseases versus healthy mothers and potential impact on the newborn – Xuanyi Meng -Journal of Crohn’s and Colitis

Human multi-site microbiome
Shared gut, but distinct oral microbiota composition in primary Sjögren’s syndrome and systemic lupus erythematosus – Taco A. van der Meulen – Journal of Autoimmunity

Urine Bacteria-Derived Extracellular Vesicles and Allergic Airway Diseases in Children – Mona Samra – International Archives of Allergy and Immunology

Review: Repertoire of bacterial species cultured from the human oral cavity and respiratory tract – Maxime DM Fonkou – Future Microbiology

Gut-brain axis
Schizophrenia and gut-flora related epigenetic factors – Chuanjun Zhuo – Progress in Neuro-Psychopharmacology and Biological Psychiatry

The structure of resilience in irritable bowel syndrome and its improvement through hypnotherapy: Cross-sectional and prospective longitudinal data – Johannes Peter – PLOS One

Fermented foods, the gut and mental health: a mechanistic overview with implications for depression and anxiety – Hajara Aslam – Nutritional Neuroscience

Chronic alcohol exposure induced gut microbiota dysbiosis and its correlations with neuropsychic behaviors and brain BDNF/Gabra1 changes in mice – Zheng Xu – Biofactors

Microbial treatment: the potential application for Parkinson’s disease – Xin Fang – Neurological Sciences

Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria. – Egle Cekanaviciute – mSystems

Human gut microbiome
The effect of drinking water pH on the human gut microbiota and glucose regulation: results of a randomized controlled cross-over intervention – Tue H. Hansen – Scientific Reports

Composition of gut microbiota and its association with body mass index and lifestyle factors in a cohort of 7–18 years old children from the American Gut Project – Jinbing Bai – Pediatric Obesity

Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans. – Bastiaan W Haak – Journal of Antimicrobial Chemotherapy

Helicobacter pylori Infection: New Facts in Clinical Management. – Peter Malfertheiner – Current Treatment Options in Gastroenterology

Animal experiments
The protective effects of fecal microbiota transplantation in an experimental model of necrotizing enterocolitis – Christian Prado – Journal of Pediatric Surgery

Intestinal Snakeskin Limits Microbial Dysbiosis during Aging and Promotes Longevity – Anna M. Salazar – iScience

Animal microbiome
Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling – Melanie M. Lloyd – Scientific Reports

Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host–Symbiont Dynamics Plasticity Affect Invasion Capacity?– Hila Dror – Microbial Ecology

Fecal bacterial microbiota of Canadian commercial mink (Neovison vison): Yearly, life stage, and seasonal comparisons – Nicole R. Compo – PLOS One

Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem – Po-Yu Liu – Microbial Ecology

Influence of Feeding Type and Nosema ceranae Infection on the Gut Microbiota of Apis cerana Workers – Shao K. Huang – mSystems

Host selectively contributes to shaping intestinal microbiota of carnivorous and omnivorous fish – Kristian Daly – The Journal of General and Applied Microbiology

Plant, root, and soil microbiome
Fire modulates ecosystem functioning through the phylogenetic structure of soil bacterial communities – Eduardo Pérez-Valera – Soil Biology and Biochemistry

Assessment of soil microbial communities involved in cellulose utilization at two contrasting Alpine forest sites – José A. Siles – Soil Biology and Biochemistry

Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach – Fen-Guo Zhang – Microbial Ecology

Influence of different biological control agents and compost on total and nitrification driven microbial communities at rhizosphere and soil level in a lettuce – Fusarium oxysporum f. sp. lactucae pathosystem – Maria Alexandra Cucu – Journal of Applied Microbiology

Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos. – Fan Wang – AMB Express

Changes in bacterial diversity and catabolic gene abundance during the removal of dimethylphenol isomers in laboratory-scale constructed wetlands. – Mónica A. Vásquez Piñeros – Applied Microbiology and Biotechnology

Abiotic factors determine functional outcomes of microbial inoculation of soils from a metal contaminated brownfield – Jay Prakash Singh – Ecotoxicology and Environmental Safety

Applying microbial biogeography in soil forensics – Habteab Habtom – Forensic Science International: Genetics

eDNA metabarcoding supporting community assessment of environmental stressor in a field-based sediment microcosm study – Jianghua Yang – Environmental Science and Technology

Water and extremophile microbiome
Analysis of the diversity of aerobic, thermophilic endospore-forming bacteria in two Algerian hot springs using cultural and non-cultural methods – Mohamed Amine Gomri – Annals of Microbiology

Anaerobic biological treatment of industrial saline wastewater: Fixed bed Reactor performance and analysis of the microbial community structure and abundance – Mariem Jeddi – Environmental Technology

Microbiome triggered transformations of trace organic chemicals in the presence of effluent organic matter in managed aquifer recharge (MAR) systems – Karin Hellauer – Environmental Science and Technology

Insights on the freshwater microbiomes metabolic changes associated with the world’s largest mining disaster – Marcelle C. Cordeiro – Science of the Total Environment

Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge – Sean Ting-Shyang Wei – mSystems

Built environment
Leaching of indium from end-of-life LCD panels via catalysis by synergistic microbial communities – Yaling Xie – Science of the Total Environment

Probiotics/Prebiotics
Probiotic and synbiotic therapy in the critically ill: State of the art – James M. Davison – Nutrition

Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers. – Leen Boesmans – mSystems

Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions – Yunus E. Tuncil – Scientific Reports

Bioinformatics
Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks – Demetrius DiMucci – mSystems

Techniques
A tridecaptin-based fluorescent probe for differential staining of Gram-negative bacteria. – Wei Wang – Analytical and Bioanalytical Chemistry

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity – Jeremiah J. Minich – mSystems

Book Chapter: Activity-Based Protein Profiling—Enabling Multimodal Functional Studies of Microbial Communities – Christopher Whidbey – Current Topics in Microbiology and Immunology

October 23, 2018

Here comes today’s Microbiome Digest featuring the recent articles on microbial methane oxidizers, sulfidic waters, PM exposure effect on airway microbiome, dysbiotic state of spring fever, diets targeting microbiome and be a cure, peri-implantitis, effect of age and inflammation on mice microbiome, diet effect on monkeys microbiome, fecal microbial transplant in UC patients, cervical microbiome, functional repertoire of ETEC and Bifidobacterium, bile duct inflammation causing microbes, role of probiotics. HAPPY READING.

EVENTS, JOBS, SCHOLARSHIPS:

Commonwealth PhD Scholarships – Study at UK University

ENVIRONMENTAL MICROBIOME:

Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers – He Z – Environ Pollut

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters – Deja-Sikora E – Microb Ecol

HUMAN RESPIRATORY MICROBIOME:

Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure – Wang L – Ecotoxicol Environ Saf

ORAL MICROBIOME:

Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children – Chen B – Int Immunopharmacol

The Severity of Human Peri-Implantitis Lesions Correlates with the Level of Submucosal Microbial Dysbiosis – Kröger A – J Clin Periodontol

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis – Boyer E – Sci Rep

Effects of antimicrobial peptide GH12 on the cariogenic properties and composition of a cariogenic multispecies biofilm – Jiang W – Appl Environ Microbiol
GUT MICROBIOME:

Review: Natural polysaccharides exhibit anti-tumor activity by targeting gut microbiota – Liu L – Int J Biol Macromol

Polysaccharides from Laminaria japonica alleviated metabolic syndrome in BALB/c mice by normalizing the gut microbiota – Duan M – Int J Biol Macromol.

Gut microbiota translocation promotes autoimmune cholangitis – Ma HD – J Autoimmun

Competitive lottery-based assembly of selected clades in the human gut microbiome – Verster AJ- Microbiome

Mini-Review : Leaky Gut, Leaky Brain? – Obrenovich MEM – Microorganisms

REPRODUCTIVE MICROBIOME:

Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study – Arokiyaraj S –
Sci Rep

ANIMAL MODEL MICROBIOME:

Long-term intake of Lactobacillus paracasei KW3110 prevents age-related chronic inflammation and retinal cell loss in physiologically aged mice – Morita Y – Aging

Targeted Diet Modification Reduces Multiple Sclerosis-like Disease in Adult Marmoset Monkeys from an Outbred Colony – Kap YS – J Immuno

FUNCTIONAL REPERTOIRE INSIGHTS:

Cell surface polysaccharides of Bifidobacterium bifidum induce the generation of Foxp3+ regulatory T cells – Verma R – Sci Immunol.

De-O-Acetylation of mucin-derived sialic acids by recombinant NanS-p esterases of Escherichia coli O157:H7 strain EDL933 – Feuerbaum S – Int J Med Microbiol.

PLANT MICROBIOME:

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales – Li HY- Microbiome

METHODS:

Protocol for faecal microbiota transplantation in ulcerative colitis (FMTUC): a randomised feasibility study – Jitsumura M – BMJ Open

PROBIOTICS:

Probiotics in Autoimmune and Inflammatory Disorders – Liu Y – Nutrients

NON-MICROBIOME PICK:

Preprint: Segregational drift and the interplay between plasmid copy number and evolvability – Judith Ilhan- Biorxiv

17 October,​ 2018

General Microbiome

ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling.Zhang C. Frontiers in Physiology

Skin Microbiome

The emerging role of skin microbiome in atopic dermatitis and its clinical implication.Stalder JF. Journal of Dermatological Treatment

Oral Microbiome

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.Hardy K. Environmental Anthropology

Gut Microbiome

Gut Microbial Product Predicts Cardiovascular Risk in Chronic Kidney Disease Patients.Jadoon A. American Journal of Nephrology

Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes.Luis AS. Current Opinions in Chemical Biology

Vitamin D and the gut microbiome: a systematic review of in vivo studies.Waterhouse M. European Journal of Nutrition

A Review: The Fate of Bacteriocins in the Human Gastro-Intestinal Tract: Do They Cross the Gut-Blood Barrier?Dicks LMT. Frontier in Microbiology

Precision identification of diverse bloodstream pathogens in the gut microbiome.Tamburini FB. Nature Medicine

Animal Microbiome

Rickettsia diversity in southern Africa: A small mammal perspective.Essbauer S. Tick and Tick-Borne Disease

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets.Liu B. Frontier in Microbiology

Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau.Bai X. Frontier in Microbiology

Microbiome-assisted carrion preservation aids larval development in a burying beetle.Shukla SP. PNAS

The gut microbiome: Relationships with disease and opportunities for therapy.Durack J. Journal of Experimental Medicine

Water Microbiome

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater.Fan XY. Bioresource Technology

Fine-scale spatial homogenization of microbial habitats: a multivariate index of headwater wetland complex condition.Moon JB. Ecological Applications

Functional and taxonomic classification of a greenhouse water drain metagenome.López-Leal G. Standards in Genomic Sciences

Plant and Soil Microbiome

Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels.Zhou H. Science of the Total Environment

Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation.Beckmann S. ISME Journal

October 14, 2018

General microbiome

16S rRNA Gene Analysis with QIIME2 – Michael Hall, Microbiome Analysis

Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt – Gavin M. Douglas, Microbiome Analysis

Single-Cell Genomics of Microbial Dark Matter – Christian Rinke, Microbiome Analysis

An ecosystem framework for understanding and treating disease – Michael E. Hochberg, Foundation for Evolution, Medicine, and Public Health

Diet, Gut Microbes and Host Mate Choice – Philip T. Leftwich, BioEssays

Pregnancy and early life

Methods and Strategies to Examine the Human Breastmilk Microbiome – Lauren LeMay-Nedjelski, Microbiome Analysis

Multi-site human microbiome

Potential mechanisms linking gut microbiota and portal hypertension – Gyorgy Baffy, Liver International

Enlisting commensal microbes to resist antibiotic-resistant pathogens –  James W. Keith, Journal of Experimental Medicine

Human oral microbiome

Oral mucosa-on-a-chip to assess layer-specific responses to bacteria and dental materials – Christopher Rahimi, Biomicrofluidics

The effect of breastmilk and saliva combinations on the in vitro growth of oral pathogenic and commensal microorganisms – E. L. Sweeney, Scientific Reports

Human skin microbiome

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes – David L. A. Wood, mBio

Human gut microbiome

The microbiome of Crohn’s disease aphthous ulcers – Claire L. O’Brien, Gut Pathogens

Gut microbiome can be restored without adverse events after Helicobacter pylori eradication therapy in teenagers – Takuji Gotoda, Helicobacter

Animal microbiome

Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere – Alejandra Hernandez-Agreda, mBio

Host differentiation and compartmentalization of microbial communities in the azooxanthelate cupcorals Tubastrea coccinea and Rhizopsammia goesi in the Caribbean – Aschwin H. Engelen, Frontiers in Microbiology

Comparison of intestinal microbes in female and male Chinese concave‐eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities – Yilin Shu, Microbiology Open

Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of Eriocheir sinensis – Chenhe Wang, Microbiology Open

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging – Marie Lisandra Zepeda Mendoza, Acta Veterinaria Scandinavica

Animal experiments 

Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury – Saisai Cheng, mSystems

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows – Gareth Frank Difford, Plos Genetics

Inhibitory effects of dietary soy isoflavone and gut microbiota on contact hypersensitivity in mice – Takao Nagano, Food Chemistry

Lichen microbiome

Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota – Tomislav Cernava, ISME

Plant, root, and soil microbiome

Short-term effect of Eucalyptusplantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange – Caroline A. Cuer, Scientific Reports

Microbial community structure and functional potential of lava-formed Gotjawal soils in Jeju, Korea – Jong-Shik Kim, Plos One

Diversity of fungi and bacteria in species-rich grasslands increases with plant diversity in shoots but not in roots and soil – Diana Navrátilová, FEMS Microbiology Ecology

Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas – Maarten Van Geel, FEMS Microbiology Ecology

Influence of triazole pesticides on tillage soil microbial populations and metabolic changes – Praveen Satapute, Science of The Total Environment

Soil Nutrient Status and Microbial Communities as Influenced by Bio-Fuel Trees Plantation – Agnes Imoya P. O., Environment and Ecology

Various Phyllosphere and Soil Bacterial Communities of Natural Grasses and the Impact Factors in a Copper Tailings Dam – Tong Jia, Current Microbiology

Effects of wine-cap Strophariacultivation on soil nutrients and bacterial communities in forestlands of northern China – Sai Gong, PeerJ

Effect of pH and temperature on microbial community structure and carboxylic acid yield during the acidogenic digestion of duckweed – Ozgul Calicioglu, Biotechnology for Biofuels

Trichoderma harzianum T-22 and BOL-12QD inhibit lateral root development of Chenopodium quinoa in axenic co-culture – Oscar M. Rollano-Peñaloza, Cogent Biology

Water, wastewater, and extremophile microbiome

Microbial communities in the nepheloid layers and hypoxic zones of the Canary Current upwelling system – Stefan Thiele, Microbiology Open

The effects of litter quality and living plants on the home-field advantage of aquatic macrophyte decomposition in a eutrophic urban lake, China – Van Biak Luai, Science of The Total Environment

The microbiome and antibiotic resistance in integrated fishfarm water: Implications of environmental public health – Gary Klase, Science of The Total Environment

Changes in the drinking water microbiome: effects of water treatments along the flow of two drinking water treatment plants in a urbanized area, Milan (Italy) – Antonia Bruno, Frontiers in Microbiology

Organic particles: heterogeneous hubs for microbial interactions in aquatic ecosystems – Mina Bizic-Ionescu, Frontiers in Microbiology

Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands – Yan Zhang, Environmental Pollution

A nearly uniform distributional pattern of heterotrophic bacteria in the Mariana Trench interior – Jiwei Tian, Deep Sea Research Part I: Oceanographic Research Papers

Patterns of permissiveness towards broad host range plasmids in microbial communities across the urban water cycle in Europe – Arnaud Dechesne, Abstract from 17th International Symposium on Microbial Ecology

Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP – Ana C. Reis, Applied Microbiology and Biotechnology

Molecular and microbiological insights on the enrichment procedures for the isolation of petroleum degrading bacteria and fungi – Giulia Spini, Frontiers in Microbiology

Microbial Ecology of South Florida Surface Waters: Examining the Potential for Anthropogenic Influences – Chase P. Donnelly, HCNSO Student Theses and Dissertations

Antarctic heterotrophic bacterium Hymenobacter nivis P3Tdisplays light‐enhanced growth and expresses putative photoactive proteins – Mia Terashima, Environmental Microbiology Reports

Microbial genomics

Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing – Robert Dyrdak, bioRxiv

Leveraging single-cell genomics to expand the fungal tree of life – Steven R. Ahrendt, Nature Microbiology

Microbes in space

Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere – Patricia Fajardo-Cavazos, Scientific Reports

Food microbiology

Metagenomic analysis and the functional profiles of traditional fermented pork fat ‘sa-um’ of Northeast India – Surajit De Mandal, AMB Express

Probiotics / prebiotics

Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP – Rodrigo Carvalho, Scientific Reports

In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota – Sophie Fehlbaum, International Journal of Molecular Sciences

Techniques

Assessing the ratio of Bacillus spores and vegetative cells by shotgun proteomics – Charlotte Mappa, Environmental Science and Pollution Research

 

4 October, 2018

Today’s digest is full of exciting wine and animal microbiome studies!😁🐌🍷

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

September 30, 2018

General microbiome

Multi-omics integrative analysis with genome-scale metabolic model simulation reveals global cellular adaptation of Aspergillus niger under industrial enzyme production condition – Hongzhong Lu, Scientific Reports

Botulinum Neurotoxin-Producing Bacteria. Isn’t It Time that We Called a Species a Species? – Theresa Smith, mBio

Sizing Up the Uncultured Microbial Majority – Laura A. Hug, mSystems

Pregnancy and early life

TLR Activation and Allergic Disease: Early Life Microbiome and Treatment – Kathryn R. Michels, Current Allergy and Asthma Reports

Human gut microbiome

Lifestyle Factors Affecting the Gut Microbiota’s Relationship with Type 1 Diabetes – Elke Gülden, Current Diabetes Reports

Animal experiments

MAVS deficiency induces gut dysbiotic microbiota conferring a proallergic phenotype – Emilie Plantamura, PNAS

Assessing microbial contamination and antibiotic resistant bacteria using zebra mussels (Dreissena polymorpha) – Maria Alexandra Bighiu, Science of The Total Environment

Plant, root, and soil microbiome

Use of sugarcane–soybean intercropping in acid soil impacts the structure of the soil fungal community – Tengxiang Lian, Scientific Reports

Aphid infestation in the phyllosphere affects primary metabolic profiles in the arbuscular mycorrhizal hyphosphere – Carmina Cabral, Scientific Reports

Antioxidative response in leaves and allelochemical changes in root exudates of Ricinus communis under Cu, Zn, and Cd stress – Shuifeng Wang, Environmental Science and Pollution Research

Biochemical and microbiological activity of soil contaminated with o-cresol and biostimulated with Perna canaliculus mussel meal – Magdalena Zaborowska, Environmental Monitoring and Assessment

Assessment of Soil Microbial Status under Different Land Use Systems in North Western Zone of Kashmir – Fozia Shafiq Wani, International Journal of Current Microbiology and Applied Sciences

Culturable Foliar Fungal Endophytes of Mangrove Species in Bicol Region, Philippines – Jonathan Jaime G. Guerrero, Philippine Journal of Science

Developmental stage has a greater effect than Cry1Ac expression in transgenic cotton on the phyllosphere mycobiome – Jiangang Pan, Canadian Journal of Microbiology

Interaction of Brassicaceae seed meal soil amendment and apple rootstock genotype on microbiome structure and replant disease suppression – Likun Wang, Phytopathology

Response of soil micro-ecology to different levels of cadmium in alkaline soil – Bin Wu, Ecotoxicology and Environmental Safety

Variation of soil bacterial communities along a chronosequence of Eucalyptusplantation – Jiayu Li, PeerJ

Long-term nitrogen fertilization elevates the activity and abundance of nitrifying and denitrifying microbial communities in an upland soil: implications for nitrogen loss from intensive agricultural systems – Fenghua Wang, Frontiers in Microbiology

Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi – Valeria Ventorino, Scientific Reports

Genome guided investigation of antibiotics producing actinomycetales strain isolated from a Macau mangrove ecosystem – Dini Hu, Scientific Reports

Water and extremophile microbiome

Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments – Man Kit Cheung, Scientific Reports

Discovering novel hydrolases from hot environments – Roland Wohlgemuth, Biotechnology Advances

Microbes in space

Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial “spaceflight response” – Michael D. Morrison, Scientific Reports

Food microbiology

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

Waste microbiome

Bioelectrochemical enhancement of methane production in anaerobic digestion of food waste – Jae-Min Choi, International Journal of Hydrogen Energy

Performance and Microbial Community Analysis of Bioaugmented Activated Sludge System for Indigo Production from Indole – Xuwang Zhang, Applied Biochemistry and Biotechnology

Probiotics / prebiotics

Bifidobacterium pseudocatenulatum CECT 7765 supplementation improves inflammatory status in insulin-resistant obese children – Jesús Sanchis-Chordà, European Journal of Nutrition

Bioinformatics

Design and implementation of semester long project and problem based bioinformatics course – Geetha Saarunya, F1000 Research

Techniques

NMR-Based Metabolomic Approach To Elucidate the Differential Cellular Responses during Mitigation of Arsenic(III, V) in a Green Microalga – Neha Arora, ACS Omega