January 15, 2019

Highlights today include the organisms in the healthy infant intestinal microbiome that protect against food allergy, an algorithm to predict aging based on the gut microbiome, and how bacteria adapt to life on the International Space Station. Enjoy!

Pregnancy and early life
Healthy infants harbor intestinal bacteria that protect against food allergy – Taylor Feehley – Nature Medicine

Human gut microbiome
Preprint: Human microbiome aging clocks based on deep learning and tandem of permutation feature importance and accumulated local effects – Fedor Galkin – bioRxiv
(Covered in popular press as Your Gut Microbiome Could Actually Reveal Your Age, Study Shows)

Preprint: The virome in adult monozygotic twins with concordant or discordant gut microbiomes – J. Leonardo Moreno-Gallego – bioRxiv

Human nearly-sterile sites
Review: Microbiome–metabolome reveals the contribution of gut–kidney axis on kidney disease – Yuan-Yuan Chen – Journal of Translational Medicine

Animal experiments
Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo-Min Jang – Molecular Nutrition and Food Research

Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats – Yun Xia – Applied Microbiology and Biotechnology

Impact of intramammary inoculation of inactivated Lactobacillus rhamnosus and antibiotics on the milk microbiota of water buffalo with subclinical mastitis – Carlotta Catozzi – PLOS One

Plant, root, and soil microbiome
Superior dispersal ability can lead to persistent ecological dominance throughout succession – Primrose J. Boynton – Applied and Environmental Microbiology

Plant growth-promoting rhizobacterium Pseudomonas PS01 induces salt tolerance in Arabidopsis thaliana – Thanh Nguyen Chu – BMC Research Notes

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ\

Antifungal potential of bacterial rhizosphere isolates associated with three ethno-medicinal plants (poppy, chamomile, and nettle) – Marija Mojicevic – International Microbiology

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions – Taotao Zeng – Environmental Science and Pollution Research

Water and extremophile microbiomes
An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community – Po-Hsiang Wang – The ISME Journal

Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients – Zhiyuan Yao – Applied and Environmental Microbiology

Effects of salinity on microbialite-associated production in Great Salt Lake, Utah – Melody R. Lindsay – Ecology

Preprint: Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria – Xiaoqin Wu – bioRxiv

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria – Maxim Rubin-Blum – mSphere

Techniques
Generation of 13C-labeled MUC5AC mucin oligosaccharides for stable isotope probing of host-associated microbial communities – Clayton Evert – ACS Infectious Diseases

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism – Hiroki Nishiguchi – Metabolic Engineering

Built environment/Microbes in Space
Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil – Ryan A. Blaustein – mSystems
(Covered in the popular press as Good news: space bacteria (probably) aren’t evolving to destroy us)

Science, publishing, and career
Preprint: Tracking the popularity and outcomes of all bioRxiv preprints – Richard J. Abdill – bioRxiv

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December 20, 2018

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

General microbiome

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

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

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

Human gut microbiome

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

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

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

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

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

Human oral microbiome

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

Animal experiments

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

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

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

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

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

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

Techniques

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

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

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

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

Microbes in the news

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

Non-microbiology picks

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

November 29, 2018

Today’s digest covers updates on human milk oligosaccharides, microbial life in cemetry, intestinal resistome, and benefits of intermittent fasting in human cohort and the gut microbiota in mice.

General microbiome
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017 – Rashmi Sinha – Microbiome

Human gut microbiome

Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection – Sasirekha Ramani – Nature Communications

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions – Caspar Bundgaard-Nielsen – Scientific Reports

In-and-Out Molecular Changes Linked to the Type 2 Diabetes Remission after Bariatric Surgery: An Influence of Gut Microbes on Mitochondria Metabolism – Paulina Samczuk – International Journal of Molecular Sciences

Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease – Takayuki Imai – Journal of Gastroenterology

Gut microbiota features of the geographically diverse Indian population – Sudarshan A. Shetty – BioRxiv

Animal experiments

Intermittent administration of a fasting-mimicking diet intervenes in diabetes progression, restores β cells and reconstructs gut microbiota in mice Siying Wei – Nutrition and Metabolism

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – Microbiome

Mouse intestinal microbiota reduction favors local intestinal immunity triggered by antigens displayed in Bacillus subtilis biofilm – Cédric M. Vogt – Microbial Cell Factories

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus – Alison Vrbanac – BMC Microbiology

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J. Kamus – PlosOne

Soil microbiome

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments – Nina Dombrowski – Nature Communications

Built Environment

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments – Akebe Luther King Abia – Science of the Total Environment

Techniques

Prediction of the intestinal resistome by a three-dimensional structure-based method – Etienne Ruppé – Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling – Ching Jian – BioRxiv

Microbes in the news

Poo found on every McDonald’s touchscreen tested – Metro

Non-microbiology picks

Effects of intermittent and continuous calorie restriction on body weight and metabolism over 50 wk: a randomized controlled trial – Ruth Schübel – The American Journal of Clinical Nutrition

 

November 27, 2018

Microbial communities of IBS patients after fecal microbiota transplantation, the shipworm gill-associated microbiota, a profile of bioartist Ani Liu in our “bacteria art” section.

Human skin microbiome

The Microbiome in Atopic Dermatitis – Amy S Paller – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Microbiome dynamics in obesity – Christoph A Thaiss – Science

The kinetics of gut microbial community composition in patients with irritable bowel syndrome following fecal microbiota transplantation – Tarek Mazzawi – PLOS ONE

Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential – Christopher Bulow – mSphere

Comparison of the gut microbiota of obese individuals from different geographic origins – Emmanouil Angelakis – New Microbes and New Infections

Review: Fire in the Forest: Adverse Effects of Antibiotics on the Healthy Human Gut Microbiome – Manosha Perera – International Journal of Medical Reviews

Animal experiments

Proteomic Analysis of Microbial Induced Redox-Dependent Intestinal Signaling – Jason D Matthews – Redox Biology

Population and Culture Age Influence the Microbiome Profiles of House Dust Mites – Jan Hubert – Microbial Ecology

Animal microbiome

Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans – Francesca Scolari – BMC Microbiology

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

Plant, root, and soil microbiome

Host-specific signatures of the cell wall changes induced by the plant parasitic nematode, Meloidogyne incognita – Refik Bozbuga – Scientific Reports

The effects of struvite and sewage sludge on plant yield and the microbial community of a semiarid Mediterranean soil – F Bastida – Geoderma

Review: Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review – Tong Yu – Science of the Total Environment

Water and extremophile microbiome

Combining fish and benthic communities into multiple regimes reveals complex reef dynamics – Mary K Donovan – Scientific Reports

Diversity and predictive metabolic pathways of the prokaryotic microbial community along a groundwater salinity gradient of the Pearl River Delta, China – Shilei Sang – Scientific Reports

Bioinformatics

Pre-print: Naught all zeros in sequence count data are the same – Justin D Silverman – bioRxiv

Microbes in the news

A bacterium’s enemy isn’t your friend – Michael S. Gilmore – Nature

Bacteria art

Portrait of the Artist as a Microbial Growth – Kevin Litman-Navarro – The Outline

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

 

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