February 16, 2019

Today’s digest is full of interesting articles about virome and phages, sinonasal microbiome and human milk microbiota. Enjoy weekend reading!

General microbiome

Bacteria and archaea on Earth and their abundance in biofilms – Hans-Curt Flemming – Nature Reviews Microbiology

The Impact of Low-FODMAPs, Gluten-Free, and Ketogenic Diets on Gut Microbiota Modulation in Pathological Conditions – Sofia Reddel – Nutrients

Impact of Gut Microbiota on Host Glycemic Control – Celine Gérard – Frontiers in Endocrinology

Intestinal Microbiota as a Host Defense Mechanism to Infectious Threats – Simona Iacob – Frontiers in Microbiology

Pregnancy and early life

Composition and Variation of the Human Milk Microbiota Are Influenced by Maternal and Early-Life Factors – Shirin Mossavi – Cell Host and Microbe

Human microbiome

Gut microbiota diversity associates with cardiorespiratory fitness in post-primary treatment breast cancer survivors – Stephen J. Carter – Experimental Physiology

Alterations in fecal short-chain fatty acids in patients with irritable bowel syndrome: A systematic review and meta-analysis – Qinghua Sun – Medicine

Mucosa-associated microbiota drives pathogenic functions in IBD-derived intestinal iNKT cells – Claudia Burrello – Life Science Alliance

The international sinonasal microbiome study (ISMS): a multi-centre, international characterization of sinonasal bacterial ecology – Sathish Paramasivan – BioRxiv

Microbiotyping the sinonasal microbiome – Ahmed Bassiouni – BioRxiv

Prevotella copri in individuals at risk for rheumatoid arthritis – Deshire Alpizar-Rodriguez – Annals of Rheumatic Diseases

Gut Microbiota Dysbiosis Is Not Independently Associated With Neurocognitive Impairment in People Living With HIV – Fengdi Zhang – Frontiers in Microbiology

Animal experiments

Gut microbiota signatures and lipids metabolism profiles by exposure to polyene phosphatidylcholine – Haining Yu – Biofactors

Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs – Jianping Quan – Frontiers in Microbiology

Plant root soil microbiome

Successive phytoextraction alters ammonia oxidation and associated microbial communities in heavy metal contaminated agricultural soils – Jipeng Luo – Science of The Total Environment

Water microbiome and extremophiles

Low concentrations of copper oxide nanoparticles alter microbial community structure and function of sediment biofilms – Lingzhan Miao – Science of the Total Environment

Characterizing the microbiome in petroleum reservoir flooded by different water sources – Xiaotong Wang – Science of the Total Environment

Baseline characterisation of aerobic hydrocarbon degrading microbial communities in deep‐sea sediments of the Great Australian Bight, Australia – Jodie van de Kamp – Environmental Microbiology

Viruses and phages

Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis – Lasha Gogokhia – Cell Host and Microbe

Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins – J. Leonardo Moreno-Gallego – Cell Host and Microbe

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome – Andrey N. Shkoporov – Cell Host and Microbe

Non-microbiology picks

Function and mechanisms of enteroendocrine cells and gut hormones in metabolism – Fiona M. Gribble – Nature Reviews Endocrinology

 

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January 31, 2019

Today’s digest covers articles describing sphingolipids in host-microbiome interaction, unique microbiome and metabolome of Indian population, selection and stabilization of soil microbiome and effect of probiotics on early sepsis in patients and immune response in childrenEnjoy reading!

General microbiome

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview – Partho Sen – Metabolites

Altered composition and function of intestinal microbiota in autism spectrum disorders: a systematic review – Feitong Liu – Translational Psychiatry

Sphingolipids in host–microbial interactions – Stacey L. Heaver – Current Opinion in Microbiology

Pregnancy and early life

Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children – Shilu Mathew – Scientific Reports

Pathways linking caesarean delivery to early health in a dual burden context: Immune development and the gut microbiome in infants and children from Galápagos, Ecuador – Amanda L. Thompson – American Journal of Human Biology

Human gut microbiome

The vagino-cervical microbiome as a woman’s life history – Zhuye Jie – BioRxiv

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers – Nielson T. Baxter – mBio

The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches – D.B. Dhakan – Gigascience

Animal experiments

Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats – Suzana Stanisavljević – Scientific Reports

Intestinal epithelial N-acylphosphatidylethanolamine phospholipase D links dietary fat to metabolic adaptations in obesity and steatosis – Amandine Everard – Nature Communications

Mutual interplay between IL-17–producing γδT cells and microbiota orchestrates oral mucosal homeostasis – Anneke Wilharm – PNAS

Plant, root and soil microbiome

Selection, succession and stabilization of soil microbial consortia – Elias K. Zegeye – BioRxiv

Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow – Mohammad Ghashghavi – BioRxiv

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance – Sammy Frenk – Applied and Environmental Microbiology

Water and extremophiles microbiome

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity – Aleksei A. Korzhenkov – Microbiome

Antibiotic disturbance affects aquatic microbial community composition and foodweb interactions but not community resilience – Ester M. Eckert – Molecular Ecology

 Phages and viruses

Megaphages infect Prevotella and variants are widespread in gut microbiomes – Audra E. Devoto – Nature Microbiology

Probiotics / prebiotics

Dysbiosis in early sepsis can be modulated by a multispecies probiotic: a randomised controlled pilot trial – V. Stadlbauer – Beneficial Microbes

Lactobacillus plantarum IS-10506 supplementation increases faecal sIgA and immune response in children younger than two years – P.D. Kusumo – Beneficial Microbes

Supplementation with Lactobacillus kefiranofaciens ZW3 from Tibetan Kefir improves depression-like behavior in stressed mice by modulating the gut microbiota – Ye Sun – Food and Function

Non-microbiology picks

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping – Helmuth Gehart – Cell

January 24, 2019

Today’s digest covers interesting reviews on microbiome and microbial metabolites, and research articles showing bacteria in meconium, how host and microbial factors affect host physiology and mechanistic insight into role of microbiota in alleviation of intestinal inflammation.

General microbiome

Review: Role of the microbiome in human development – Maria Gloria Dominguez-Bello – Gut

Review: The role of the intestinal microbiota in uremic solute accumulation: a focus on sulfur compounds – Alessandra F. Perna – Journal of Nephrology

Review: Gut microbial metabolites in obesity, NAFLD and T2DM – Emanuel E. Canfora – Nature Reviews Endocrinology

Pregnancy and early life

Characterisation of the bacterial microbiome in first‐pass meconium using propidium monoazide (PMA) to exclude non‐viable bacterial DNA – Lisa F. Stinson – Letters in Applied Microbiology

Perinatal antibiotics alter preterm infant EEG and neurobehavior in the Family Nurture Intervention trial – Morgan R. Firestein – Developmental Psychobiology

Altered gut microbiota and short chain fatty acids in Chinese children with autism spectrum disorder – Simeng Liu – Scientific Reports

Human gut microbiome

Gut microbiota density influences host physiology and is shaped by host and microbial factors – Eduardo J. Contijoch – Elife

The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response – Sydney Lavoie – Elife

Alterations in the intestinal microbiota of patients with severe and active Graves’ orbitopathy: a cross-sectional study – T. T. Shi – Journal of Endocrinological Investigation

Fecal microbiota transplantation for treatment of recurrent C. difficile infection: An updated randomized controlled trial meta-analysis – Wenjia Hui – PlosOne

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts – Nandita R. Garud – PlosBiology

MicroRNA-Mediated Tumor–Microbiota Metabolic Interactions in Colorectal Cancer – Ce Yuan – DNA and Cell Biology

Modulation of the Gut Microbiota by Resistant Starch as a Treatment of Chronic Kidney Diseases: Evidence of Efficacy and Mechanistic Insights – Matthew Snelson – Advances in Nutrition

Animal experiments

Microbiota fermentation-NLRP3 axis shapes the impact of dietary fibres on intestinal inflammation Vishal Singh – Gut

A high linoleic acid diet exacerbates metabolic responses and gut microbiota dysbiosis in obese rats with diabetes mellitus – Hsiu-Chuan Lee – Food and Function

Gut microbiota profiling with differential tolerance against the reduced dietary fibre level in rabbit – Shi-Yi Chen – Scientific Reports

Novel strains of Bacteroides fragilis and Bacteroides ovatus alleviate the LPS-induced inflammation in mice – Huizi Tan – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Consistency in microbiomes in cultures of Alexandrium species isolated from brackish and marine waters – Eva Sörenson – Environmental Microbiology Reports

Probiotics / prebiotics

Review: Beneficial Effects of Probiotic Consumption on the Immune System – C. Maldonado Galdeano – Annals of Nutrition and Metabolism

Microbes on the market

Ferring, Rebiotix and Karolinska Institutet Extend Collaboration to Research Next Generation of Microbiome Treatments – Microbiome Times

Non-microbiology picks

Those with inadequate access to food likely to suffer from obesity – Science Daily

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 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 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