Category Archives: Water microbiome

November 2, 2018

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Your Friday Digest features plentiful of soil/plant and gut microbiome papers. Highlights include correlation between infant metabolic functions and diet/gestational weight gain, profiling human gut microbiomes across India, and the absence of a placenta microbiota. There are many other more articles worth reading, enjoy!

General microbiology

Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota – Michael A. Henson & Poonam Phalak – PLoS Computational Biology

A cohabiting bacterium alters the spectrum of short RNAs secreted by Escherichia coli – Olga V Alikina et al. – FEMS Microbiology Letters

Pregnancy and early life

Long-lasting effect of oral azithromycin taken by women during labour on infant nutrition: Follow-up cohort of a randomized clinical trial in western Gambia – Anna Roca et al. – PLoS One

** Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes – Aimee M. Baumann-Dudenhoeffer et al. – Nature Medicine

Antibiotic and acid-suppression medications during early childhood are associated with obesity – Christopher M Stark et al. – Gut

** Lack of detection of a human placenta microbiome in samples from preterm and term deliveries – Jacob S. Leiby et al. – Microbiome

Human oral microbiome

Multi-species oral biofilm promotes reconstructed human gingiva epithelial barrier function – Lin Shang et al. – Scientific Reports

Review: Administration of systemic antibiotics during non-surgical periodontal therapy—a consensus report – B. Pretzl et al. – Clinical Oral Investigations

Human repiratory microbiome

Sputum Microbiome is Associated with 1-Year Mortality Following COPD Hospitalizations – Fernando Sergio Leitao Filho et al. – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The co-existence of elevated high sensitivity C-reactive protein and homocysteine levels is associated with increased risk of metabolic syndrome: A 6-year follow-up study – Jinkwan Kim & Sangshin Pyo – PLoS One

** LogMPIE, pan-India profiling of the human gut microbiome using 16S rRNA sequencing – Ashok Kumar Dubey et al. – Scientific Data

Association between Neutrophil-to-Lymphocyte Ratio and Gut Microbiota in a Large Population: a Retrospective Cross-Sectional Study – Hee-Young Yoon et al. – Scientific Reports

Microbial nitrogen limitation in the mammalian large intestine – Aspen T. Reese et al. – Nature Microbiology

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles – Trishla Sinha et al. – Gut Microbes

Anti-Inflammatory Activities of Pentaherbs formula and Its Influence on Gut Microbiota in Allergic Asthma – Miranda Sin-Man Tsang et al. – Molecules

Identification of TMAO-producer phenotype and host–diet–gut dysbiosis by carnitine challenge test in human and germ-free mice – Wei-Kai Wu et al. – Gut

Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin – Zhen He et al. – Gut

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers – Vanessa L. Hale et al. – Genome Medicine

Comment: Targeting the microbiome: from probiotics to fecal microbiota transplantation – Alexander Khoruts – Genome Medicine

Human vaginal microbiome

Review: Endometrial microbes and microbiome: Recent insights on the inflammatory and immune “players” of the human endometrium – Silvia D’Ippolito et al. – American Journal of Reproductive Immunology

Animal experiments

Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs – Mathilde Le Sciellour et al. – PLoS One

Effects of ultraviolet radiation and nutrient level on the physiological response and organic matter release of the scleractinian coral Pocillopora damicornis following thermal stress – Lucile Courtial et al. – PLoS One

Dog: Balance of saccharolysis and proteolysis underpins improvements in stool quality induced by adding a fiber bundle containing bound polyphenols to either hydrolyzed meat or grain-rich foods – Matthew I. Jackson & Dennis E. Jewell – Gut Microbes

Ventilator-induced lung injury is aggravated by antibiotic mediated microbiota depletion in mice – Sandra-Maria Wienhold & Mario Macrì et al. – Critical Care

Mouse: Dioxin-like PCB 126 increases intestinal inflammation and disrupts gut microbiota and metabolic homeostasis – Michael C. Petriello et al. – Environmental Pollution

Review: Innate Immune Influences on the Gut Microbiome: Lessons from Mouse Models – Susan J. Robertson et al. – Trends in Immunology

Animal microbiome

Milk microbiome diversity and bacterial group prevalence in a comparison between healthy Holstein Friesian and Rendena cows – Paola Cremonesi & Camilla Ceccarani et al. – PLoS One

Comparing the bacterial communities of wild and captive golden mantella frogs: Implications for amphibian conservation – Luiza F. Passos et al. – PLoS One

Insect anal droplets contain diverse proteins related to gut homeostasis – Tianzhong Jing et al. – BMC Genomics

Plant, root and soil microbiome

Putative Nitrogen-fixing bacteria Associated with The Rhizosphere and Root Endosphere of wheat plants grown in an Andisol from southern Chile – Joaquin I. Rilling et al. – Frontiers in Microbiology

Land-use intensity rather than plant functional identity shapes bacterial and fungal rhizosphere communities – Ricardo Schöps et al. – Frontiers in Microbiology

Microbial expression profiles in the rhizosphere of two maize lines differing in N use efficiency – Shamina Imran Pathan et al. – Plant and Soil

The rhizosphere of the halophytic grass Sporobolus robustus Kunth hosts rhizobium genospecies that are efficient on Prosopis juliflora (Sw.) DC and Vachellia seyal (Del.) P.J.H. Hurter seedlings – Fatoumata Fall et al. – Systematic and Applied Microbiology

Rhizosphere responses to environmental conditions in Radix pseudostellariae under continuous monoculture regimes – Hongmiao Wu et al. – Agriculture, Ecosystems & Environment

Plant-microbe interactions endorse growth by uplifting microbial community structure of Bacopa monnieri rhizosphere under nematode stress – Rupali Gupta et al. – Microbiological Research

Review: Multifaceted interactions between endophytes and plant: Developments and Prospects – Naveen K. Arora et al. – Frontiers in Microbiology

Enhancing phytoextraction of HMs at real scale, by combining Salicaceae Trees with microbial consortia – CARMINE GUARINO et al. – Frontiers in Environmental Science

PhD Dissertation: Implications of land-use legacy on soil microbiomes of urban grasslands – Grant Lafayette Thompson – Cornell University

Body size determines soil community assembly in a tropical forest – Lucie Zinger et al. Molecular Ecology

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes – Joshua Ladau et al. – mSystems

Water and extremophile microbiome

Microbial diversity and antibiotic resistance in a final effluent-receiving lake – Kinga Bondarczuk & Zofia Piotrowska-Seget – Science of The Total Environment

Non‐random processes determine the colonization of groundwater sediments by microbial communities in a pristine porous aquifer – Lucas Fillinger et al. – Environmental Microbiology

Food microbiome

Changes of microbial community and metabolite in kimchi inoculated with different microbial community starters – Seong-Eun Park et al. – Food Chemistry

Phages and viruses

Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow – A. Bal et al. – BMC Infectious Diseases

Technology

A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples – Matthew V. Cannon et al. – Microbiome

Bioinformatics

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification – Daniel J. Nasko et al. – Genome Biology

* Species-level functional profiling of metagenomes and metatranscriptomes – Eric A. Franzosa et al. – Nature Methods

Striped UniFrac: enabling microbiome analysis at unprecedented scale – Daniel McDonald et al. – Nature Methods

Mechanistic microbiota models – Tal Nawy – Nature Methods

Microbes in the news

Club STEAM Powered students study bacteria, genetics – Cassie Gibb – The Southeast Sun

Media alert: New articles in The CRISPR Journal – MARY ANN LIEBERT, INC. – EurekAlert!

Electric shocks kill bacteria – Vienna University of Technology – PHYS.org

The Mad Science of Fermentation’s Funky Flavors – Joe Ray – Wired

How Nuclear Testing Transformed the Land in Nevada and New Mexico – Kealey Boyd – Hyperallergic

October 28, 2018

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Featured today: Social & population health science approaches towards human microbiome; sinus microbiome; gut microbiota-dietary phytoestrogen relationship in captive rhinos; halophytes- soil microbiome link in the river delta; microbial shift in bioreactor during methanogenesis; gut bacterium of fruit fly alters locomotory activity by one of its isomerases.

General microbiome

Review: Feather degradation by keratinolytic bacteria and biofertilizing potential for sustainable agricultural production – K. Tamreihao – Journal of Basic Microbiology

Social and population health science approaches to understand the human microbiome – Pamela Herd – Nature Human Behaviour

Human respiratory microbiome

The effect of maxillary sinus antrostomy size on the sinus microbiome – Alexander S. Kim BSE – International Forum of Allergy & Rhinology

Human oral microbiome

Parvimonas micra stimulates expression of gingipains from Porphyromonas gingivalis in multi-species communities – Jessica Neilands – Anaerobe

Human gut microbiome

Microbiota stability in healthy individuals after single-dose lactulose challenge—A randomized controlled study – Sandra Y. Wotzka – PLoS One

Timing for the second fecal microbiota transplantation to maintain the long-term benefit from the first treatment for Crohn’s disease – Pan Li – Applied Microbiology and Biotechnology

Spatial and Temporal Analysis of the Stomach and Small Intestinal Microbiota in Fasted Healthy Humans – Anna Seekatz – bioRxiv

Prospective Study of Oral Microbiome and Colorectal Cancer Risk in Low‐income and African American Populations – Yaohua Yang – International Journal of Cancer

Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure – Joann Romano-Keeler – PLoS One

Animal experiments 

Effects of water decontamination methods and bedding material on the gut microbiota – Willie A. Bidot – PLoS One

The Oral Microbiota Is Modified by Systemic Diseases – DT Graves – Journal of Dental Research

Gut microbiome disruption altered the biotransformation and liver toxicity of arsenic in mice – Liang Chi – Archives of Toxicology

Salmonella shedding status of the sow affects the microbiota of their piglets at weaning – Guillaume Larrivière‐Gauthier – Journal of Applied Microbiology

Mixture of Two Lactobacillus plantarum Strains Modulates the Gut Microbiota Structure and Regulatory T Cell Response in Diet‐Induced Obese Mice – Jieun Lee – Molecular Nutrition and Food Research

Animal microbiome 

Habitat-specific variation in gut microbial communities and pathogen prevalence in bumblebee queens (Bombus terrestris) – L Bosmans – PLoS One

Influence of midgut microbiota in Anopheles stephensi on Plasmodium berghei infections – Devaiah Monnanda Kalappa – Malaria Journal

Host blood meal source has a strong impact on gut microbiota of Aedes aegypti – Ephantus J Muturi – FEMS Microbiology Ecology

Gut microbiota and phytoestrogen-associated infertility in southern white rhinoceros – Candace L Williams – bioRxiv

Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany – Tim Boehmer – PLoS One

Proteome and microbiota analysis reveals alterations of liver-gut axis under different stocking density of Peking ducks – Yuqin Wu – PLoS One

Plant, root, and soil microbiome

Oxygen loss from seagrass roots coincides with colonisation of sulphide-oxidising cable bacteria and reduces sulphide stress – Belinda C. Martin – The ISME Journal

Coastal halophytes alter properties and microbial community structure of the saline soils in the Yellow River Delta, China – Changliang Jing – Applied Soil Ecology

Enumeration, Antagonism and Enzymatic Activities of Microorganisms Isolated from Railway Station Soil – Megha Sharma – bioRxiv

Bacterial survival strategies in an alkaline tailing site and the physiological mechanisms of dominant phylotypes as revealed by metagenomic analyses – Weimen Sun – Environmental Science & Technology

Water and extremophile microbiome 

Assessment of Anthropogenic Influence on Antarctic Mycobiota in Areas of Russian Polar Stations – I. Yu. Kirtsideli – Contemporary Problems of Ecology

Built environment 

Simulation of in situ oil reservoir conditions in a laboratory bioreactor testing for methanogenic conversion of crude oil and analysis of the microbial community – Dan Xu – International Biodeterioration & Biodegradation

Phages and viruses

Bacteriophages shift the focus of the mammalian microbiota – Breck A. Duerkop – PLoS Pathogens

Virome Analysis Reveals No Association of Head and Neck Vascular Anomalies with an Active Viral Infection – Nora Franke – In Vivo

Bacteriophages dynamically modulate the gut microbiota and metabolome – Bryan B. Hsu – bioRxiv

Techniques

Rapid differentiation of Lactobacillus species via metabolic profiling – Kundi Yang – Journal of Microbiological Methods

Modelling the role of microbial p-cresol in colorectal genotoxicity – Eiman Abdulla Al Hinai – Gut Microbes

Microbes in the news

Gut microbes alter the walking activity of fruit flies – Nature

October 23, 2018

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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

October 22, 2018

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Today’s digest features a novel fecal species [Prevotella rara sp. nov.], the virome in feces from healthy children from three Amerindian villages with minimal outside contact, a review of statistical challenges in the design and analysis of longitudinal microbiome studies, and more. Happy reading!

Gut microbiome

*Prevotella rara sp. nov., isolated from human faeces – Boris A. Efimov – International Journal of Systematic and Evolutionary Microbiology

Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women – Eveliina Munukka – Frontiers in Microbiology

Association of serum bilirubin in newborns affected by jaundice with gut microbiota dysbiosis – Shaoming Zhou – The Journal of Nutritional Biochemistry

Review: Gut-microbiota-on-a-chip: an enabling field for physiological research – Grissel Trujillo-de Santiago – MicroPhysiological Systems

Review: Microbiome and diabetes: Where are we now? – Natalia G. Vallianou – Diabetes Research and Clinical Practice

Oral microbiome

Review: Biology of Oral Streptococci – Jacqueline Abranches – Microbiology Spectrum

Animal and plant microbiome

Review: How Can We Define “Optimal Microbiota?”: A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture – Wakako Ikeda-Ohtsubo – Frontiers in Nutrition

Water microbiome

Temperature-controlled thermophilic bacterial communities in hot springs of western Sichuan, China – Jie Tang – BMC Microbiology

In situ production of core and intact bacterial and archaeal tetraether lipids in groundwater – Su Ding – Organic Geochemistry

Phages and viruses

*Complex virome in feces from Amerindian children in isolated Amazonian villages – Juliana D. Siqueira – Nature Communications

Bioinformatics

*Preprint Review: Statistical Considerations in the Design and Analysis of Longitudinal Microbiome Studies – Justin D Silverman – bioRxiv

October 19, 2018

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Today’s Digest provides much food for thought. Highlights include how to identify keystone species, a seminal review on the long-term and short-term effects of C-section on mom and child’s health, and a new de novo assembler for short metagenomic reads.

General microbiology

Antibiotic export by efflux pumps affects growth of neighboring bacteria – Xi Wen et al. – Scientific Reports

Proteomic analysis of four Clostridium botulinum strains identifies proteins that link biological responses to proteomic signatures – Brooke L. Deatherage Kaiser et al. – PLoS One

Biodiversity‐function relationships in methanogenic communities – Pawel Sierocinski et al. – Molecular Ecology

Solubilization and degradation of polychlorinated biphenyls (PCBs) by naturally occurring facultative anaerobic bacteria – Gathanayana Pathiraja et al. – Science of the Total Environment

An improved neutral community model for temporal observations in microbial communities – Li Jie & Shen Xuzhu – Ecological Modelling

** Identifying Keystone Species In The Microbial Community Based On Cross-sectional Data – Min Li et al. – Current Gene Therapy

Does quorum sensing interference affect the fitness of bacterial pathogens in the real world? – Yiying Liu et al. – Environmental Microbiology

Pregnancy and early life

Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow’s Milk Protein Allergy under a Restricted Diet – María Díaz et al. – Nutrients

** Review: Short-term and long-term effects of caesarean section on the health of women and children – Jane Sandall et al. – Lancet

Human skin microbiome

The Skin Microbiota in Patients Hospitalized for Cellulitis and Association With Outcome – Duncan R Cranendonk et al. – Clinical Infectious Diseases

Human multi-site microbiome

Continuous Antibiotic Prophylaxis in Pediatric Urology – Douglas W.Storm et al. – Urologic Clinics of North America

Human gut microbiome

Impact of antibiotic use on survival in patients with advanced cancers treated on immune checkpoint inhibitor phase I clinical trials – S Sen et al. – Journal of Experimental Medicine

Review: Visceral pain: gut microbiota, a new hope? – Matteo M Pusceddu & Melanie G Gareau – Journal of Biomedical Science

Review: Vulnerability of long-term care facility residents to Clostridium difficile infection due to microbiome disruptions – Beth Burgwyn Fuchs et al. – Future Microbiology

Fecal Microbiota Transplant for Recurrent Clostridium Difficile Infection in Pediatric Inflammatory Bowel Disease – Cho, Stanley et al. – Journal of Pediatric Gastroenterology and Nutrition

Transcriptome meta-analysis identifies immune signature comprising of RNA binding proteins in ulcerative colitis patients – Saima Naz et al. – Cellular Immunology

Alterations of Gut Microbiome in the Patients With Severe Fever With Thrombocytopenia Syndrome – Honghai Xu et al. – Frontiers in Microbiology

Review: Role of Gut Microbiota in the Development and Treatment of Colorectal Cancer – LIN C. et al. – Digestion

Human gut-microbiome-brain axis

A primer on investigating the role of the microbiome in brain and cognitive development – Caroline Kelsey et al. – Developmental Psychology

Animal experiments

Grape polyphenols reduce gut-localized reactive oxygen species associated with the development of metabolic syndrome in mice – Peter Kuhn et al. – PLoS One

Host developmental toxicity of BPA and BPA alternatives is inversely related to microbiota disruption in zebrafish – Tara R Catron et al. – Toxicological Sciences

Liver Injury, Endotoxemia, and Their Relationship to Intestinal Microbiota Composition in Alcohol-Preferring Rats – Brunella Posteraro et al. – Alcoholism Clinical & Experimental Research

Liver tumorigenesis is promoted by a high saturated-fat diet specifically in male mice and is associated with hepatic expression of the proto-oncogene Agap2 and enrichment of the intestinal microbiome with Coprococcus – Kim B Pedersen et al. – Carcinogenesis

Animal microbiome

Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises – Chava L. Weitzman et al. – Royal Society Open Science

Review: Understanding the Milk Microbiota – Stephanie A.Metzger et al. – Veterinary Clinics of North America: Food Animal Practice

Evolution of the nasopharyngeal bacterial microbiota of beef calves from spring processing to 40 days after feedlot arrival – Christopher McMullen et al. – Veterinary Microbiology

Plant, root and soil microbiome

Review: The impact of microbes in the orchestration of plants’ resistance to biotic stress: a disease management approach – Matthew Chekwube Enebe & Olubukola Oluranti Babalola – pplied Microbiology and Biotechnology

Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts – Xuepeng Sun et al. New Phytologist

Facilitation promotes invasions in plant-associated microbial communities – Wei, Zhong et al. – Ecology Letters

Water and extremophile microbiome

Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations – David A. Aromokeye et al. – Frontiers in Microbiology

Bacterial community changes in a glacial-fed Tibetan lake are correlated with glacial melting – Keshao Liu et al. – Science of The Total Environment

Food microbiology

Review: Fermentation trip: amazing microbes, amazing metabolisms – Rong Feng et al. – Annals of Microbiology

Phages and viruses

Complete Genome Sequence of the Model Halovirus PhiH1 (ΦH1) – Mike Dyall-Smith et al. – Genes

Technology

Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer – Sae Ashikawa et al. – Journal of Medical Microbiology

The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study – Jan Tkadlec et al. – Clinical Microbiology and Infection

Bioinformatics

BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results – Aitor Blanco-Míguez et al. – PLoS One

Review: Integrating–omics data into genome-scale metabolic network models: principles and challenges – Charlotte Ramon et al. – Essays in Biochemistry

** High-quality genome sequences of uncultured microbes by assembly of read clouds – Alex Bishara et al. – Nature Biotechnology

Microbes in the news

Cecilia Jonsson Serenades Sewage Bacteria – Sofia Bergmann – Berlin Art Link

October 18, 2018

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Today’s digest covers articles on the potential of fecal microbiota transplant in obesity and Crohn’s disease, modeling approach to address interactions in simplified microbial community, news on antibiotic resistance and a gigantic single cell transcriptomics database encompassing twenty mouse organs!

General Microbiome

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community – Kevin D’hoe – eLife

The role of the lung microbiota and the gut‐lung axis in respiratory infectious diseases – Alexia Dumas – Cellular Microbiology

Gut microbiota and obesity: An opportunity to alter obesity through Fecal Microbiota Transplant (FMT) – Patrick Lee – Diabetes Obesity and Metabolism

Human gut microbiome

Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants – Katri Korpela – Microbiome

Diversified gut microbiota in newborns of mothers with gestational diabetes mellitus – Minglian Su – PlosOne

Gut dysbiosis with Bacilli dominance and accumulation of fermentation products precedes late-onset sepsis in preterm infants – S Graspeuntner – Clinical Infectious Diseases

The Safety of Fecal Microbiota Transplantation for Crohn’s Disease: Findings from A Long-Term Study – Honggang Wang – Advances in Therapy

Animal experiments

Effect of dietary Spirulina (Arthrospira) platensis on the growth performance, antioxidant enzyme activity, nutrient digestibility, cecal microflora, excreta noxious gas emission, and breast meat quality of broiler chickens – J H Park – Poultry Science

Water and extremophile microbiome

Differential incorporation of one-carbon substrates among microbial populations identified by stable isotope probing from the estuary to South China Sea – Wenchao Deng – Scientific Reports

Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System – I. Mania – Microbial Ecology

Community composition of nitrous oxide reducing bacteria investigated using a functional gene microarray – A. Jayakumar – Deep Sea Research Part II: Topical Studies in Oceanography

Built environment

Microbial and Metabolic Succession on Common Building Materials Under High Humidity Conditions – Simon Lax – BioRxiv

Bioinformatics/Techniques

Designing metabolic division of labor in microbial communities – Meghan Thommes – BioRxiv

Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives – Anna-Lena Heins – Bioprocess and Biosystems Engineering

Hydrogenotrophic methanogens of the mammalian gut: functionally similar, thermodynamically different. A modelling approach – Rafael Munoz-Tamayo – BioRxiv

Microbes in the news

Most burger chains fail on annual antibiotics report card – CNN

Sales of antibiotics for use in food-producing animals drop across the EU – European Medicine Agencies News

Non-microbiology picks

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris – The Tabula Muris Consortium – Nature

17 October,​ 2018

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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

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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

 

October 11, 2018

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The effects of chronic ethanol ingestion on the fruit fly microbiota, engineering the mosquito microbiota to produce an antiplasmodial effector, how temperature change affects an ecosystems biodiversity and function.

General microbiome

Changes in temperature alter the relationship between biodiversity and ecosystem functioning – Francisca C García – PNAS

Human respiratory microbiome

Respiratory Microbiota Predicts Clinical Disease Course of Acute Otorrhea in Children With Tympanostomy Tubes – Wing Ho Man – The Pediatric Infectious Disease Journal

Human oral microbiome

Carious status and supragingival plaque microbiota in hemodialysis patients – Qi Yue – PLOS ONE

Human gut microbiome

Review: Fecal Microbiota Transplantation for the Management of Clostridium difficile Infection – Raghavendra Paknikar – Surgical Infections

Review: Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients – Chih-Yu Yang – Nephrology

Animal experiments

Risks Related to High-Dosage Recombinant Antimicrobial Peptide Microcin J25 in Mice Model: Intestinal Microbiota, Intestinal Barrier Function and Immune Regulation – Haitao Yu – Journal of Agricultural and Food Chemistry

Microbial Changes and Host Response in F344 Rat Colon Depending on Sex and Age Following a High-Fat Diet – Sun Min Lee – Frontiers in Microbiology

Animal microbiome

Pre-print: Chronic ethanol ingestion impairs Drosophila melanogaster health in a microbiome-dependent manner – James Angus Chandler – bioRxiv

Blood meal-induced inhibition of vector-borne disease by transgenic microbiota – Jackie L Shane – Nature Communications

Plant, root, and soil microbiome

Friends or foes in the rhizosphere: traits of fluorescent Pseudomonas that hinder Azospirillum brasilense growth and root colonization – Guillermo A Maroniche – FEMS Microbiology Ecology

Water and extremophile microbiome

Seasonal variation of extracellular enzymatic activity in marine snow-associated microbial communities and their impact on the surrounding water – Ingrid Ivančić – FEMS Microbiology Ecology

Food microbiology

Comparative evaluation of spoilage-related bacterial diversity and metabolite profiles in chilled beef stored under air and vacuum packaging – Ahmad Rois Mansur – Food Microbiology

Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl – Ilenys M Pérez-Díaz – Food Microbiology

Bioinformatics

Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo – Katherine A Dunn – Microbiome Analysis (Book)

Metabolomics

Targeted Metabolic Profiling Indicates Apple Rootstock Genotype-Specific Differences in Primary and Secondary Metabolite Production and Validate Quantitative Contribution From Vegetative Growth – Rachel Leisso – Frontiers in Plant Science

Techniques

Analyzing Metabolic Pathways in Microbiomes – Mobolaji Adeolu – Microbiome Analysis (Book)

More microbes

Prevalence of Yersinia Species in the Ileum of Crohn’s Disease Patients and Controls – Guillaume Le Baut – Frontiers in Cellular and Infection Microbiology

October 10, 2018

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Microbiota conservation and diversity in butterfly species, air and waterborne microbiota of a pharmaceutical plant, the a study on the oral microbiota of rugby players.

General microbiome

Preserving microbial diversity – Maria G Dominguez Bello – Science

Pregnancy and early life

Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy – Kristine M Wylie – BMC Research Notes

Human skin microbiome

The microbiome of the “sterile” pustules in palmoplantar pustulosis – Kana Masuda-Kuroki – Experimental Dermatology

Human oral microbiome

Oral health and microbiota status in professional rugby players: A case-control study – Matthieu Minty – Journal of Dentistry

Oral Bacteriome Compositions Identified by 16S rRNA Metagenomics in a Randomly Selected “Healthy” Nigerian Male and Female Subjects – Kingsley C Anukam – International Journal of Research and Reports in Dentistry

Human gut microbiome

Review: The Gut-Brain Axis and the Microbiome: Mechanisms and Clinical Implications – Vadim Osadchiy – Clinical Gastroenterology and Hepatology

Animal experiments

Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota – Kathryn Eaton – eLIFE

Animal microbiome

Pre-print: Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – PeerJ

Gastrointestinal Microbial Flora in Wild and Captive Olive Baboons (Papio anubis) – Senelwa Davis Lugano – American Journal of Infectious Diseases and Microbiology

Plant, root, and soil microbiome

Rhizosphere microbiome structure alters to enable wilt resistance in tomato – Min-Jung Kwak – Nature Biotechnology

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition – Xiaofen Chai – Journal of Applied Microbiology

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing – Huan Li – Journal of Basic Microbiology

Ectomycorrhizal fungi may not act as a barrier inhibiting host plant absorption of heavy metals – Yangze Tang – Chemosphere

Pre-print: Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances – Rodrigo G Taketani – PeerJ

Water and extremophile microbiome

Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas – NV Pimenov – Microbiology

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles – Sheila Powell – The ISME Journal

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing – Otakar Strunecky – Extremophiles

Built environment

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

Food microbiology

Review: The Effect of Gluten-Free Diet on Health and the Gut Microbiota Cannot Be Extrapolated from One Population to Others – Jose F Garcia-Marzcorro – Nutrients

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – MN Weber – Virology

Bioinformatics

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets – Bhusan K Kuntal – The ISME Journal

Techniques

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus – Matthew E Mokszycki – Applied and Environmental Microbiology

Science, career, and publishing

Inoculating science against potential pandemics and information hazards – Kevin M Esvelt – PLOS Pathogens