Category Archives: Microbes in the News

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 25, 2018

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Roller coaster of fantastic articles today! Two sister articles from TEDDY cohort about development of the gut microbiota in early childhood and type-1 diabetes. Another article on association of the early gut microbiota with body mass index later in life in a Norwegian cohort. A multi-omics study of the rumen microbiota and insight into how human gut microbiota recovers following antibiotic exposure. And many more, keep reading…

Human gut microbiome

Recovery of gut microbiota of healthy adults following antibiotic exposure – Albert Palleja – Nature Microbiology

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study – Tommi Vatanen – Nature

Temporal development of the gut microbiome in early childhood from the TEDDY study – Christopher J. Stewart – Nature

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort – Maggie A. Stanislawski – mBio

Human gut microbe co-cultures have greater potential than monocultures for food waste remediation to commodity chemicals – Matthew A. Perisin – Scientific Reports

Animal experiments

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem – Lindsey M. Solden – Nature Microbiology

A gut microbial factor modulates locomotor behaviour in Drosophila – Catherine E. Schretter – Nature

Dietary fibers inhibit obesity in mice, but host responses in the cecum and liver appear unrelated to fiber-specific changes in cecal bacterial taxonomic composition – Janice E. Drew – Scientific Reports

Plant, root, and soil microbiome

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

Techniques

Intestinal barrier dysfunction orchestrates the onset of inflammatory host–microbiome cross-talk in a human gut inflammation-on-a-chip – Woojung Shin – PNAS

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon – Anna Cusco – BioRxiv

Microbes in the news

3 million common procedures in England could become ‘life threatening’ without antibiotics – CNN

Antibiotic plus probiotic combination may kill off superbugs – Medical News Today

Microbes on the market

Microbiotica Attracts Equity Investment from Seventure’s Health for Life Capital Fund – Microbiome Times

Rebiotix and Microbiome Insights Collaborate on a Microbiome IBD Tool for Clinical Development – Microbiome Times

APC Microbiome Ireland pool resources to lead maternity probiotic venture – Nutraingredients.com

Non-microbiology picks

How should autonomous vehicles be programmed? – ScienceDaily

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

October 02, 2018

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Today’s digest features a study on altered gut microbial composition in persons with chronic schizophrenia, a review of different approaches for discovering radical-dependent enzymes in the human gut microbiota and Nature podcast with the latest science news. Happy reading/listening!

Gut microbiome

*Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects – Tanya T. Nguyen – Schizophrenia Research

*Review: Discovering radical-dependent enzymes in the human gut microbiota – Benjamin J Levin and Emily P Balskus – Current Opinion in Chemical Biology

Review: Air Pollution, Early Life Microbiome, and Development – Yvonne Vallès and M. Pilar Francino – Current Environmental Health Reports

Review: The implementation of omics technologies in cancer microbiome research – Benjamin H Mullish – Ecancermedicalscience

Skin microbiome

Skin microbiome modulation induced by probiotic solutions – Bernhard Paetzold – bioRxiv

Vaginal microbiome

Review: Alternative and complementary therapies for vulvovaginal candidiasis – Thais Chimati Felix – Folia Microbiologica

Animal microbiome

Review: Fish Gut Microbiome: Current Approaches and Future Perspectives – Chandni Talwar – Indian Journal of Microbiology

Review: The application of omics to rumen microbiota function – Stuart E Denman – Animal

Animal experiments

The circadian clock regulates the diurnal levels of microbial short‐chain fatty acids and their rhythmic effects on colon contractility in mice – Anneleen Segers – Acta Physiologie

Bioinformatics

Dynamic interaction network inference from longitudinal microbiome data – Jose Lugo-Martinez – bioRxiv

Microbes in the news

6 Artificial Sweeteners That Can Hurt Your Microbiome Revealed in New Study – By Emma Betuel – Inverse

Study: Measuring Artificial Sweeteners Toxicity Using a Bioluminescent Bacterial Panel – Dorin Harpaz – Molecules

Podcast

*A wearable biosensor and a metamaterial’s strange behaviour – Benjamin Thompson and Shamini Bundell – Nature Podcast

September 26, 2018

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Today’s mid-week short digest includes articles on integrating human genetics and the gut microbiome to find potent risk factors in cardiovascular disease; comparison of bariatric surgery techniques on the gut microbiota; transmission of antibiotic resistance genes from mothers to infants and importance of breastfeeding. News updates on growth prediction of human microbiome based diagnostics and first rapid test to determine Bifidobacteria in infant gut!

Human gut microbiome

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome – Daria V. Zhernakova – Nature Genetics

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements – Katariina Pärnänen – Nature Communications

Multidrug-resistant Gram-negative bacteria from patients, hospital environment and healthcare workers: a six-month cross-sectional study – Aline Fernanda Rodrigues Sereia – bioRxiv

Microbiota stability in healthy individuals after single-dose lactulose challenge – a randomized controlled study – Sandra Y Wotzkas – bioRxiv

Laparoscopic Roux-en-Y gastric bypass profoundly changes gut microbiota compared to laparoscopic sleeve gastrectomy: a metagenomic comparative analysis – William Farin – bioRxiv

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer – PlosOne

Profiling of microorganism-binding serum antibody specificities in professional athletes – Rajna Minić – PlosOne

Animal experiments

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets – John J Miklavcic – The Journal of Nutrition

Glyphosate perturbs the gut microbiota of honey bees – Erick V. S. Motta – PNAS

Water and extremophile microbiome 

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of Solfatara Crater (Campi Flegrei, southern Italy) – Crognale Simona – Fems Microbiology Ecology

Techniques

The Smallest Intestine (TSI) – a low volume in vitro model of the small intestine with increased throughput – T Cieplak – FEMS microbiology Letters

Microbes in the news

First-Ever Rapid Response Test for Levels of Bifidobacterium in Baby’s Gut Microbiome – Microbiome Times

Human Microbiome Market will Likely to expanding at a CAGR of 9.8% during the forecast period from 2018 to 2026 – Business Analyst

Puppies spread antibiotic-resistant infections to 118 people, CDC reports – CBS News

Non-microbiology picks

The best of intentions: Prenatal breastfeeding intentions and infant health – Kerri M. Raissian – SSM Population Health

 

September 24, 2018

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General microbiology

Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine – Jason Merritt, PHYSICAL REVIEW LETTERS

Small at Size, Big at Impact: Microorganisms for Sustainable Development – Nasib Singh, Microbial Bioprospecting for Sustainable Development

Population Genomics of Archaea: Signatures of Archaeal Biology from Natural Populations – David J. Krause, Population Genomics

Pregnancy and early life

Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum – Aina Gotoh, Scientific Reports

Multi-site human microbiome

Gut–Liver Axis: How Do Gut Bacteria Influence the Liver? – Peter Christopher Konturek, Medical Sciences

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer, Plos One

Optimal immunosuppressor induces stable gut microbiota after liver transplantation – Jian-Wen Jiang, World Journal of Gastroenterology

Human respiratory microbiome

The Microbiome and Tuberculosis: Early Evidence for Cross Talk – Sivaranjani Namasivayam, mBio

Trans-maternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T-cells – Andreas Kyburz, Journal of Allergy and Clinical Immunology

Human oral microbiome

Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situbiofilm model – Stefan Rupf, Scientific Reports

Human gut microbiome

In silico Identification of Metagenomic Signature Describing Neurometabolic Potential of Normal Human Gut Microbiota – A. S. Kovtun, Russian Journal of Genetics

Gut microbiota modulates drug pharmacokinetics – Juanhong Zhang, Drug Metabolism Reviews

Active Site Flexibility Revealed in Crystal Structures of Parabacteroides merdae β‐Glucuronidase from the Human Gut Microbiome – Michael S. Little, Protein Science

Structural and Functional Analysis of the Gut Microbiome for Toxicologists – Robert G. Nichols, Current Protocols in Toxicology

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet, Neurogastroenterology and Motility

Animal experiments

Response of goose intestinal microflora to the source and level of dietary fiber – Haizhu Zhou, Poultry Science

Microbiota modulation by eating patterns, dietary and macronutrient composition; impact on food intake – Elizabeth A. Klingbeil, American Journal of Physiology

Water and extremophile microbiome

Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking – Moa Hägglund, Frontiers in Microbiology

Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N – Beatriz Fernández-Gómez, ISME

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean – Francisco Martinez-Hernandez, ISME

Microbial Community Function in Electroactive Biofilm-based Constructed Wetlands – Ramírez Vargas, Biogeosciences

Fungal endophyte‐infected leaf litter alters in‐stream microbial communities and negatively influences aquatic fungal sporulation – Emily R. Wolfe, Synthesising Ecology

Salt marsh denitrification is impacted by oiling intensity six years after the Deepwater Horizon oil spill – Corianne Tatariw, Environmental Pollution

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination – Blaise P. Bougnom, Environmental Research

Plant, root, and soil microbiome

Phosphate solubilizing bacteria with glucose dehydrogenase gene for phosphorus uptake and beneficial effects on wheat – Muhammad Suleman, Plos One

Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests – Pengyu Zhao, PeerJ

Aphid Colonization Affects Potato Root Exudate Composition and the Hatching of a Soil Borne Pathogen – Grace A. Hoysted, Frontiers in Plant Sciences

Root inoculation with Azotobacter chroococcum 76A enhances tomato plants adaptation to salt stress under low N conditions – Michael James Van Oosten, BMC Plant Biology

Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France) – Jorge R. Osman, Antonie van Leeuwenhoek

Plant roots alter microbial functional genes supporting root litter decomposition – Shengjing Shi, Soil Biology and Biochemistry

Bacterial community response to a preindustrial‐to‐future CO2 gradient is limited and soil‐specific in Texas Prairie grassland – Swastika Raut, Global Change Biology

Built environment

Houseplants as home health monitors – C. Neal Stewart Jr., SYNTHETIC BIOLOGY

Characterization of Aspergillus niger Isolated from the International Space Station – Jillian Romsdahl, mSystems

Food microbiology

Microbiological Changes during Ripening of Chihuahua Cheese Manufactured with Raw Milk and Its Seasonal Variations – Cristina Sánchez-Gamboa, Foods

Supplementation in mushroom crops and its impact on yield and quality – Jaime Carrasco, AMB Express

Aronia (Aronia melanocarpa) Polyphenols Modulate Microbial Community in Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) and Decrease Secretion of Pro‐Inflammatory Markers in a Caco‐2/endothelial Cell Co‐Culture Model – Ting Wu, Molecular Nutrition and Food Research

Techniques

A critical evaluation of the use of gas chromatography- and high performance liquid chromatography-mass spectrometry techniques for the analysis of microbial metabolites in human urine after consumption of orange juice – José Luis Ordóñez, Journal of Chromatography A

Recovering cellular biomass from fluids using chemical flocculation – Paul A. Kenward, Environmental Microbiology Reports

Influence of support media supplementation to reduce the inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier, Data in Brief

A resourceful methodology to profile indolic auxins produced by rhizo-fungi using spectrophotometry and HPTLC – Dhavalkumar Patel, Biotech

Bioinformatics

Computational Tools and Databases of Microbes and Its Bioprospecting for Sustainable Development – Dipannita Hazra, Microbial Bioprospecting for Sustainable Development

Metabolomics

Paradoxes in leaky microbial trade – Yoav Kallus, Nature Communications

Antibiotics

Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen – Gleb Pishchany, PNAS

Microbes in the news

Subculture show converts Storefront for Art and Architecture into living lab – The Architects Newspaper, Ali Oriaku

September 20, 2018

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Today’s digest presents reviews covering potential of microbiome in olfactory communication and oral-gut microbiome axis in rheumatoid arthritis; articles on association of human gut microbiome with different diseases; news on antibiotics and scientific data on personality types in humans.

General microbiome

Review: The Extended Genotype: Microbially Mediated Olfactory Communication – Alexandra J.R. Carthey – Trends in Ecology and Evolution

Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Commmentary: Regulating stool for microbiota transplantation – Pilar N Ossorio – Gut microbes

Proteomics and the microbiome: pitfalls and potential – Huafeng Lin – Expert Review of Proteomics

Pregnancy and early life

Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children – Mon H. Tun – Canadian Medical Association Journal

Human gut microbiome

Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes, MODY2, and Healthy Control Subjects: A Case-Control Study – Isabel Leiva-Gea – Diabetes Care

Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China – Mengxiang Zhang – Scientific Reports

Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer – Marta Mangifesta – Scientific Reports

Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation – Christopher Staley – Microbiome

Could fecal phenylacetic and phenylpropionic acids be used as indicators of health status? – Isabel Gutiérrez-Díaz – Journal of Agricultural and Food Chemisty

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet – Neurogastroenterology and Motility

Animal experiments

Melatonin reprogramming of gut microbiota improves lipid dysmetabolism in high fat diet-fed mice – Jie Yin – Journal of Pineal Research

Water and extremophile microbiome

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake – Keith Arora-Williams – Microbiome

Probiotics/Prebiotics

The Impact of Probiotic Supplements on Cognitive Parameters in Euthymic Individuals with Bipolar Disorder: A Pilot Study – Eva Z Reininghaus – Neuropsychobiology

Microbes in the news

The case for expensive antibiotics – http://www.wired.com

Crucial antibiotics still used on US farms despite public health fear – The Guardian

Non-microbiology picks

A robust data-driven approach identifies four personality types across four large data sets – Martin Gerlach – Nature Human Behaviour

 

September 18, 2018

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Quite a few articles of interest today:

  1. Foods that are protective of the gut microbiome: Specific oligosaccharides in breast milk can compensate for the effects of C-section births, and cranberries can compensate for the effects of dietary changes in mice.
  2. A possible bi-directional relationship between the gut microbiome and high altitudes: Specific differences in the gut microbiome are associated with differences in tolerance to high altitudes in males, and exposure to high altitudes can alter the gut microbiome in mice.
  3. Microbes in Space: Nitrogen cycle nicroorganisms that may be able to produce food, water and O2 in space, and exposing desert extremophiles to Martian conditions to learn about the kinds of bacteria on other planets

Also: How smoking impacts the lung virome, the association between fecal microbiome profile and phylogeny in deer genera, and the development of the dust microbiome over time in a classroom

Pregnancy and early life

*Fucosylated oligosaccharides in mother’s milk alleviate the effects of caesarean birth on infant gut microbiota – Katri Korpela – Scientific Reports

The influence of maternal vaginal flora on the intestinal colonization in newborns and 3-month-old infants – Iwona Gabriel – The Journal of Maternal-Fetal & Neonatal Medicine

Fecal Volatile Organic Compounds in Preterm Infants Are Influenced by Enteral Feeding Composition – Sofia el Manouni el Hassani – Sensors

Multi-site human microbiome

Review: Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Human respiratory microbiome

*Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome – Ann C. Gregory – Respiratory Research

Human anal microbiome

Anal microbial patterns and oncogenic HPV in a pilot study of Nigerian men who have sex with men at risk for or living with HIV – Rebecca G Nowak – AIDS Research and Human Retroviruses

Human gut microbiome

*Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – American Journal of Physiology

Intestinal barrier integrity in patients with plaque psoriasis – Mariusz Sikora – The Journal of Dermatology

Review: Mechanisms by which gut microorganisms influence food sensitivities
– Alberto Caminero – Nature Reviews Gastroenterology & Hepatology

Review: Selective sensitivity of the gut microbiome to iron chelators in polybacterial abdominal sepsis – Kayle Dickson – Medical Hypotheses

Review: ADHD-originating in the gut? The emergence of a new explanatory model – Anna M. Sandgren – Medical Hypotheses

Review: Guideline for the Management of Clostridium Difficile Infection in Children and Adolescents With Cancer and Pediatric Hematopoietic Stem-Cell Transplantation Recipients – Caroline Diorio – Journal of Clinical Oncology

Review: Altered Gut Microbiota in Type 2 Diabetes: Just a Coincidence? – Antonio Sircana – Current Diabetes Reports

Review: Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut? – Hanne L.P. Tytgat – Trends in Microbiology

Review: Fecal microbiota transplant – a new frontier in inflammatory bowel disease – Sunkara T – Dove Press

Review: Gut microbiota, cognitive frailty and dementia in older individuals: a systematic review –  Ticinesi A – Dove Press

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Animal experiments

Deletion of poly(ADP‑ribose) polymerase-1 changes the composition of the microbiome in the gut – András Vida – Molecular Medicine Reports

Lactobacillus reuteri F‐9‐35 Prevents DSS‐Induced Colitis by Inhibiting Proinflammatory Gene Expression and Restoring the Gut Microbiota in Mice – Mao‐cheng Sun – Journal of Food Science

*Cranberries attenuate animal-based diet-induced changes in microbiota composition and functionality: A randomized crossover controlled feeding trial – Jose Rodríguez-Morató – The Journal of Nutritional Biochemistry

*The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice – Wei Zhang – PLOS ONE

The Effects of Berberine on the Gut Microbiota in Apc min/+ Mice Fed with a High Fat Diet – Huan Wang – Molecules

The influence of gut microbiota dysbiosis to the efficacy of 5-Fluorouracil treatment on colorectal cancer – Lu Yuan – Biomedicine & Pharmacotherapy

Protein deficiency reduces efficacy of oral attenuated human rotavirus vaccine in a human infant fecal microbiota transplanted gnotobiotic pig model – Ayako Miyazaki – Vaccine

In vitro experiments

Butyrate upregulates the TLR4 expression and the phosphorylation of MAPKs and NK‑κB in colon cancer cell in vitro – Tengfei Xiao – Oncology Letters

Animal microbiome

Comparison of the gut microbiota of captive common bottlenose dolphins, Tursiops truncatus in three aquaria – Akihiko Suzuki – Journal of Applied Microbiology

Bacteria richness and antibiotic-resistance in bats from a protected area in the Atlantic Forest of Southeastern Brazil – Vinícius C. Cláudio – PLOS ONE

*Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae – Jiaying Li – Frontiers in Microbiology

Probiotics modify body weight together with anxiety states via pro-inflammatory factors in HFD-treated Syrian golden hamster – Ennio Avolio – Behavioural Brain Research

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics – Jong Nam Kim – Asian-Australas Journal of Animal Sciences

The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency – Chloe Matthews – Gut

MicrobesEvaluation of conjunctival microbiota in clinically normal persian squirrels (Sciurus Anomalus) – Houman Faghihi – Journal of Zoo and Wildlife Medicine

Plant, root, and soil microbiome

Trichoderma gamsii affected herbivore feeding behaviour on Arabidopsis thaliana by modifying the leaf metabolome and phytohormones – Dongmei Zhou – Microbial Biotechnology

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Soil microbial response to Rhododendron understory removal in southern Appalachian forests: Effects on extracellular enzymes – Ernest D. Osburn – Soil Biology and Biochemistry

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

Bacterial diversity in rhizosphere of Paspalum scrobiculatum L. (kodo millet) is revealed with shotgun metagenome sequencing and data analysis – Ratna Prabha – Data in Brief

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Microbial Ecology

Effects of Cd, Cu, Zn and their combined action on microbial biomass and bacterial community structure – Jiuwei Song – Environmental Pollution

Effects of graphene oxides and silver-graphene oxides on aquatic microbial activity – Kwanyoung Ko – Science of The Total Environment

Built environment

*Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten – Anders B. Nygaard – Microbiome

Microbiological analysis of contact lens cases: impact of the hospital environment – Vinicius Targa Villas Bôas – Arquivos Brasileiros de Oftalmologia

Microbes in space

*Nitrogen cycle microorganisms can be reactivated after Space exposure – Ralph E. F. Lindeboom – Scientific Reports

*Desert cyanobacteria under space and planetary simulations: a tool for searching for life beyond Earth and supporting human space exploration – Daniela Billi – International Journal of Astrobiology

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Bioinformatics

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis – Gherman V. Uritskiy – Microbiome

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations  – Alex N Salazar – Bioinformatics

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Microbes in the news

The electrifying energy of gut microbes – Laty A. Cahoon – Nature News and Views

Bacteria and Art

How Anicka Yi’s Science Experiments Are Expanding the Boundaries of Art – Andrew Russeth – W

 

 

August 31, 2018

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Today’s digest features the rumen microbiome from a culturomics point of view, case study of Lactobacillus and Bifidobacterium strains that helped a boy with short bowel syndrome, aging cheese in Murray’s urban caves, and much more. And, check out my non-microbiology pick that can help you become a better writer! Happy September!

Human microbiome

Worldwide Variation in Human Milk Metabolome: Indicators of Breast Physiology and Maternal Lifestyle? – Melvin C. L. Gay – Nutrients

Animal microbiome

*Insights Into Culturomics of the Rumen Microbiome – Tamar Zehavi – Front. Microbiol.

Review: Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present and future – Sharon Ann Huws – Front. Microbiol.

Lactic acid treatment of by-products and phosphorus level in the diet modulate bacterial microbiome and the predicted metagenome functions using the rumen simulation technique – Barbara U.Metzler-Zebeli – Journal of Dairy Science

Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons) – Wenzel Marius – PLoS One

Probiotics

*D-lactic Acidosis: Successful Suppression of D-lactate–Producing Lactobacillus by Probiotics – Bahtiyar Yilmaz – Paediatrics

Cholesterol-lowering effect of Lactobacillus rhamnosus BFE5264 and its influence on the gut microbiome and propionate level in a murine model – Soyoung Park – PLoS One

Effects of lactoferrin on neonatal pathogens and Bifidobacterium breve in human breast milk – Tabitha Woodman – PLoS One

Water microbiome

Nitrifying and Denitrifying Bacterial Communities in Advanced Nitrogen-Removal Onsite Wastewater Treatment Systems – Sara Wigginton – Journal of Environmental Quality – Environmental Microbiology

Soil microbiome

Preprint: Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities – Paul Carini – bioRxiv

Microbes in the news

*The Art and Science of Aging Cheese – Crystal Shi – The Epoch Times

Svetlana’s non-microbiology pick

*A great and neat tips list for all interested in better writing: Five common writing mistakes new scientists make – Jacquelyn Gill