February 14, 2019

If you are feeling butterflies in your stomach today, it might not be a gut microbiome imbalance – you might’ve caught the love bug! Happy Valentines Day!  Today’s digest features some human gut/FMT studies, a few animal gut biome studies and a couple probiotic publications.  Enjoy!

General microbiome

The next step towards anticancer microbiota therapeutics – Ursula Hofer – Nature Reviews [letter]

Expanding diversity of the human microbiome – Andrea Du Toit – Nature Reviews [in brief]

FMT in the clinic – Ashley York – Nature Reviews [research highlight]

Human respiratory microbiome

Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects – Anny Camelo-Castillo – Frontiers in Microbiology

Human gut microbiome

Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome – Daniel E. Almonacid – PLoS One

[pre -print] The Human Nickel Microbiome and its relationship to Allergy and Overweight in Women – Elena Angela Lusi – bioRxiv

The Relationship between Platelet Count and Host Gut Microbiota: A Population-Based Retrospective Cross-Sectional Study – Hee-Yong Yoon – Journal of Clinical Medicine

Data-driven multiple-level analysis of gut-microbiome-immune-joint interactions in rheumatoid arthritis – QuanQiu Wang – BMC Genomics

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes – J. Alfredo Blakeley-Ruiz – BMC Microbiome

Role of the Gut Microbiome in Autism Spectrum Disorders – Joby Pulikkan – Reviews on Biomarker Studies in Psychiatric and Neurodegenerative Disorders

Faecal microbiota transplantation in Australia: bogged down in regulatory uncertainty – Samuel P. Costello – Internal Medicine Journal

Animal experiments

Characterization of oral microbiota in marmosets: Feasibility of using the marmoset as a human oral disease model – Sachiko Takehara – PLoS One

The Effect of Multispecies Probiotic Supplementation on Iron Status in Rats – Katazyna Skrypnik – Biological Trace Element Research

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples – Susakul Palakawong Na Ayudthaya – Current Microbiology

Animal microbiome

A Diverse Microbial Community Supports Larval Development and Survivorship of the Asian Tiger Mosquito (Diptera: Culicidae) – Nicholas V Travanty – Journal of Medical Entomology

Plant, root, and soil microbiome

Belowground biota responses to maize biochar addition to the soil of a Mediterranean vineyard – Pilar Andrés – Science of The Total Environment

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining – Markus Gastauer – Scientific Data

Probiotics / prebiotics

Infant Complementary Feeding of Prebiotics for the Microbiome and Immunity – Starin McKeen – Nutrients

Techniques

Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis – James B. Thissen – PLoS One

Microbes in the news

Tube pollution: Could bacteria create clean air on the London Underground?

Ed’s non-microbiology picks

Adjunctive vitamin D in tuberculosis treatment: meta-analysis of individual participant data – David A. Jolliffe – European Respiratory Journal

Physical activity protects against depression

Want Healthier Eating Habits? Start with a workout

GMO Cassava Can Provide Iron, Zinc To Malnourished African Children

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December 26, 2018

Holidays, Happiness and some updates on the microbiome!
Today’s short digest covers functions of different Lactobacillus strains; how weaning stress affects the gut microbiome and association of bacterial metabolite TMAO with Alzheimer’s disease.

General microbiome

Review: Antibiotics and the nervous system: More than just the microbes? – Kevin Champagne-Jorgensen – Brain, Behavior, and Immunity

Human gut microbiome

The gut microbiota-derived metabolite trimethylamine N-oxide is elevated in Alzheimer’s disease – Nicholas M. Vogt – Alzheimer’s Research & Therapy

A novel probiotic, Lactobacillus johnsonii 456, resists acid and can persist in the human gut beyond the initial ingestion period – Michael J. Davoren – Gut Microbes

Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa – Mun Fai Loke – PlosOne

Human oral/respiratory microbiome

The Salivary Microbiome: Analysis of by Pyrosequencing and the Relationship with Helicobacter pylori Infection – Yingjie Ji – bioRxiv

Differences in the lower airway microbiota of infants with and without cystic fibrosis – Katherine B. Frayman – Journal of Cystic Fibrosis

Animal experiments

A Diet-Sensitive Commensal Lactobacillus Strain Mediates TLR7-Dependent Systemic Autoimmunity – Daniel F. Zegarra-Ruiz – Cell Host and Microbe

The gut microbiome is required for full protection against acute arsenic toxicity in mouse models – Michael Coryell – Nature Communications

Weaning Stress Perturbs Gut Microbiome and Its Metabolic Profile in Piglets – Yuan Li – Scientific Reports

Plant root soil microbiome

The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory – Charley J. Hubbard – Molecular Ecology

Enrichment of Verrucomicrobia, Actinobacteria and Burkholderiales drives selection of bacterial community from soil by maize roots in a traditional milpa agroecosystem – Eneas Aguirre-von-Wobeser – PlosOne

Non-microbiology picks

Friend and foe: β-cell Ca2+ signaling and the development of diabetes – Paul V. Sabatini – Molecular Metabolism

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 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

 

November 7, 2018

There’s lots of new work to catch up on! Some highlights include the skin virome in patients with immune deficiency, a mechanism for host-microbe mutualism in zebrafish, ecological pressures in soil that lead to smaller genomes, and a book chapter about the future of microbial forensics.

General Microbiome
Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness – Wen C. Aw – PLOS Genetics

Antifungal immune responses: emerging host–pathogen interactions and translational implications – Vinod Kumar – Genome Medicine

Pregnancy and early life
Childhood Adversity Impact on Gut Microbiota and Inflammatory Response to Stress During Pregnancy. – Liisa Hantsoo – Brain, Behavior, and Immunity

Enabling precision medicine in neonatology, an integrated repository for preterm birth research – Marina Sirota – Scientific Data

Associations of birth mode with cord blood cytokines, white blood cells, and newborn intestinal bifidobacteria – Isabel Cristina Ribas Werlang – PLOS One

HPV infection and bacterial microbiota in breast milk and infant oral mucosa – Heidi Tuominen – PLOS One

Human skin microbiome
Expanded skin virome in DOCK8-deficient patients – Osnat Tirosh – Nature Medicine

Microbiological Profile of Sarecycline: A Novel Targeted Spectrum Tetracycline for the Treatment of Acne Vulgaris – George Zhanel – Antimicrobial Agents and Chemotherapy

Human vaginal microbiome
Preprint: Glycan cross-feeding drives mutualism between Fusobacterium and the vaginal microbiota – Kavita Agarwal – bioRxiv

Human multi-site microbiome
The altered human serum metabolome induced by a marathon – Zinandré Stander – Metabolomics

The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media
Andrea Coleman
Microbiome

Human gut microbiome
An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men – Abigail J. S. Armstrong – Microbiome

Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: A randomized clinical trial – Zhi-Dong Jiang – PLOS One

The long term effect of metabolic profile and microbiota status in early gastric cancer patients after subtotal gastrectomy – Xi-Hsuan Lin – PLOS One

Animal experiments
A bacterial immunomodulatory protein with lipocalin-like domains facilitates host–bacteria mutualism in larval zebrafish – Annah S Rolig – eLife

Gut microbiota and intestinal FXR mediate the clinical benefits of metformin – Lulu Sun – Nature Medicine

Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model – Kazuyuki Kasahara – Nature Microbiology

Enteric infection coupled with chronic Notch pathway inhibition alters colonic mucus composition leading to dysbiosis, barrier disruption and colitis – Ishfaq Ahmed – PLOS One

Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A. Hatter – PLOS One

Plant, root, and soil microbiome
Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient – Jackson W. Sorensen – Nature Microbiology

Decomposition responses to climate depend on microbial community composition -Sydney I. Glassman – PNAS

The nanotechnology among US: are metal and metal oxides nanoparticles a nano or mega risk for soil microbial communities? – J. Parada – Critical Reviews in Biotechnology

Water and extremophile microbiome
Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia. – Nyok-Sean Lau – Microbial Ecology

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient – Alexandra Meziti – The ISME Journal

Probiotics
Anti-diabetic effects of Lactobacillus casei fermented-yogurt through re-shaping gut microbiota structure in type 2 diabetic rats – Ling Qu – Journal of Agricultural and Food Chemistry

Probiotics-fermented Massa Medicata Fermentata ameliorates weaning stress in piglets related to improving intestinal homeostasis – Yanbo Wang – Applied Microbiology and Biotechnology

Techniques
Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling – Fei Teng – Scientific Reports

Science career/training and publishing
Preprint: The CURE for Culturing Fastidious Microbes – Arundhati Bakshi – bioRxiv

Meeting Report: Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. – Jacquelyn S. Meisel -Microbiome

In win for open access, two major funders won’t cover publishing in hybrid journals

Microbial Forensics
Book Chapter: Unique Individualistic Microflora: The Future of DNA Fingerprinting Technique – Pankaj Shrivastava – DNA Fingerprinting: Advancements and Future Endeavors

Alyson’s non-microbiology picks
Science candidates prevail in US midterm elections

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 1, 2018

To kick off October, we have a Microbiome Digest filled with ecological approaches to microbial communities and techniques for analysis. Plus: what the Nobels are doing to encourage diversity, and what ecstasy does to octopuses. Happy reading!

General Microbiome
Neutral and selective dynamics in a synthetic microbial community. – Nate J. Cira – PNAS

Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology. – Elizabeth Theresa Miller – Trends in Ecology and Evolution

Clinician Guide to Microbiome Testing – Christopher Staley – Digestive Diseases and Sciences

Human Urinary Microbiome
NMR-based metabonomic approach reveals changes in the urinary and fecal metabolome caused by resveratrol. – Gabriela Torres Santiago – Journal of Pharmaceutical and Biomedical Analysis

Urinary microbes and postoperative urinary tract infection risk in urogynecologic surgical patients – Krystal J. Thomas-White – International Urogynecology Journal

Human Gut Microbiome
Metagenomic insights into resistant starch degradation by human gut microbiota. – Marius Vital – Applied and Environmental Microbiology

Pathogenic functions of host microbiota. – Silke Rath – Microbiome

Prebiotics and Probiotics in Digestive Health – Eamonn M.M. Quigley – Clinical Gastroenterology and Hepatology

Animal Experiments
Isolation and characterization of the Bacillus cereus BC7 strain, which is capable of zearalenone removal and intestinal flora modulation in mice. – Yue Wang – Toxicon

Sulfated Polysaccharide from Sea Cucumber and its Depolymerized Derivative Prevent Obesity in Association with Modification of Gut Microbiota in High‐Fat Diet‐Fed Mice – Zhenjun Zhu – Molecular Nutrition and Food Research

Animal Microbiome
Cultivable microbiome and its resistance to antimicrobials isolated from Zaprionus indianus – Graziele Aparecida Fernandes da Cruz – Environmental Monitoring and Assessment

Plant, root, and soil microbiome
Impact of weather conditions, leaf age and irrigation water disinfection on the major epiphytic bacterial genera of baby spinach grown in an open field – Pilar Truchado – Food Microbiology

Influence of light on plant – phyllosphere interaction – Sofia D. Carvalho – Frontiers in Plant Science

Techniques
PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. – Fabian Bonk – Journal of Microbiological Methods

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. – Johannes Alneberg – Microbiome

Progress of analytical tools and techniques for human gut microbiome research – Eun-Ji Song – Journal of Microbiology

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

Science, Publishing, and Career
What the Nobels are — and aren’t — doing to encourage diversity – Elizabeth Gibney -Nature

Alyson’s Non-Microbiology Pick
What Ecstasy Does to Octopuses – Ed Yong – The Atlantic