November 14, 2018

Today’s digest is about how dietary shifts and low gluten diet changes the intestinal microbiome, fecal microbiota transplant in intestinal disorders, characterization of the most abundant bacteriophage family in the human gut, and Raman spectroscopy based method for fast identification of antibiotic resistance bugs.

Human gut microbiome

Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis – Yinghong Wang – Nature Medicine

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults – Lea BS Hansen – Nature Communications

Resilience of human gut microbial communities for the long stay with multiple dietary shifts – Hong Liu – Gut

Microbiome and its relation to gestational diabetes – Ramon V. Cortez – Endocrine

Effect of bifidobacterium breve A-1 on anxiety and depressive symptoms in schizophrenia: A proof-of-concept study – Ryo Okubo – Journal of Affective Disorders

Fecal Akkermansia muciniphila Is Associated with Body Composition and Microbiota Diversity in Overweight and Obese Women with Breast Cancer Participating in a Presurgical Weight Loss Trial – Andrew D Fruge – Journal of the Academy of Nutrition and Dietetics

An Open-Labeled Study on Fecal Microbiota Transfer in Irritable Bowel Syndrome Patients Reveals Improvement in Abdominal Pain Associated with the Relative Abundance of Akkermansia Muciniphila – Cruz-Aguliar RM – Digestion

Animal experiments

Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids – Shi-Jun Yue – American Journal of Physiology Endocrinology and Metabolism

Air microbiome

A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations – Joan Cáliz – PNAS

Phages and viruses

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis – Andrey N Shkoporov – Nature Communications

Techniques

Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples – Yuan Gao – Nature Methods

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts – Justin D Silverman – Microbiome

Microbes in the news

Chinese scientists develop novel instrument for rapid profiling of antimicrobial resistance – EurekaAlert

Microbes on the market

Chr. Hansen Receives Joint Innovation Fund Grant to Develop Next Generation Microbial Solutions for Agriculture – Microbiome times

Non-microbiology picks

Remission of Human Type 2 Diabetes Requires Decrease in Liver and Pancreas Fat Content but Is Dependent upon Capacity for β Cell Recovery – Roy Taylor – Cell Metabolism

 

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October 28, 2018

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

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 18, 2018

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

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

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

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