January 10, 2020

In today’s weekend post- maternal antibodies targeting microbiota protect mice from neonatal infection, exercise improves gestational diabetes in rodent models, bacterial signature in NAFLD and TMAO as negative predictor of human embryo quality. Happy reading and a nice weekend!

General microbiome

Adolescence and aging: impact of adolescence inflammatory stress and microbiota alterations on brain development, aging and neurodegeneration – Nour Yahfoufi – The Journal of Geronotology

Preclinical and clinical relevance of probiotics and synbiotics in colorectal carcinogenesis: a systematic review – Bruna C.S. Cruz – Nutrition Reviews

Gut microbiota: a new piece in understanding hepatocarcinogenesis – An Zhou – Cancer Letters

Gut Microbiota, Diet, and Chronic Diseases: The Role Played by Oxidative Stress – Elisardo C. Vasquez – Oxidative Medicine and Cellular Longevity

New insights on the colonization of the human gut by health-promoting bacteria – Sinead T. Morrin – Applied Microbiology and Biotechnology

Human microbiome

Salivary microbiota and inflammation‐related proteins in patients with psoriasis – Daniel Belstrøm – Oral Diseases

Oral butyrate does not affect innate immunity and islet autoimmunity in individuals with longstanding type 1 diabetes: a randomised controlled trial – Pieter F. de Groot – Diabetologia

Fusobacterium nucleatum in the colorectum, and its association with cancer risk and survival: a systematic review and meta-analysis – Christian Gethings-Behncke – Cancer Epidemiology Biomarkers and Prevention

Potential impact of removing metronidazole from treatment armamentarium of mild acute Clostridioides difficile infection – Shani Zilberman-Itskovich – Future Medicine

Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease Silvia Sookoian – Gut

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels – Mohammad Tauqeer Alam – Gut Pathogens

Early life microbiota

Antibiotic Resistance Genes in the Gut Microbiota of Children with Autistic Spectrum Disorder as Possible Predictors of the Disease – Alexey S. Kovtun – Microbial Drug Resistance

Trimethylamine-N-oxide is present in human follicular fluid and is a negative predictor of embryo quality – R.A.Nagy – Human Reproduction

Animal experiments

Microbiota-targeted maternal antibodies protect neonates from enteric infection – Wen Zheng – Nature

Characterization of metabolic and inflammatory profiles of transition dairy cows fed an energy-restricted diet – Giulia Esposito – Journal of Animal Science

Microbiota dependent production of butyrate is required for the bone anabolic activity of PTH – Jau-Yi Li – Journal of Clinical Investigation

Betaine addition as a potent ruminal fermentation modulator under hyperthermal and hyperosmotic conditions in vitro – Mubarik Mahmood – Journal of the Science of Food and Agriculture

Investigating temporal microbial dynamics in the rumen of beef calves raised on two farms during early life – Eóin O’Hara – FEMS Microbial Ecology

Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization – Matthew K. Schnizlein – mSphere

Post‐natal co‐development of the microbiota and gut barrier function follows different paths in the small and large intestine in piglets – Alexis Pierre Arnaud – Faseb Journal

Phellinus linteus polysaccharide extract improves insulin resistance by regulating gut microbiota composition – Yangyang Liu – Faseb Journal

Exercise improves metabolic function and alters the microbiome in rats with gestational diabetes – Dayana Mahizir – Faseb Journal

Microbial reconstitution reverses early female puberty induced by maternal high-fat diet during lactation – Mengjie Wang – Endocrinology

Fecal microbiota as a noninvasive biomarker to predict the tissue iron accumulation in intestine epithelial cells and liver – Bingdong Liu – Faseb Journal

Techniques

Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles – Yali Liang – mSphere

May 21, 2019

Today’s digest is short and sweet but includes interesting articles. A brilliant essay on multidisciplinarity in microbiome research 🥰

General Microbiome

ESSAY: Multidisciplinarity in Microbiome Research: A Challenge and Opportunity to Rethink Causation, Variability, and Scale. KR Amato – BioEssays

REVIEW:Contribution of the Mucosal Microbiota to Bovine Respiratory HealthM Zeineldin. Trends in Microbiology

Characterization of a novel salt-, xylose-and alkali-tolerant GH43 bifunctional β-xylosidase/α-l-arabinofuranosidase from the gut bacterial genome. B Xu. Journal of Bioscience and Bioengineering

Gut Microbiome

Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular CarcinomaEJ Cho. Scientific Reports

The bacterial communities of the small intestine and stool in children with short bowel syndrome. SL Zeichner. PLOS ONE

Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approachesGA Lugli. BMC Genome Biology

Plant, Soil, and Water Microbiome

Microbial production and consumption of dissolved organic matter in glacial ecosystems on the Tibetan PlateauL Zhou. Water Research

Engineering banana endosphere microbiome to improve Fusarium wilt resistance in banana. Y Liu.Microbiome
Toxic responses of metabolites, organelles and gut microorganisms of Eisenia fetida in a soil with chromium contaminationR Tang. Environmental Pollution

Roles of microbes in supporting sustainable rice production using the system of rice intensificationF Doni. Applied Microbiology and Biotechnology

Cover crop species have contrasting influence upon soil structural genesis and microbial community phenotype.A Bacq-Labreuil. Scientific Reports

Preprint

Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn’s Disease Cohort . Daniel Sprockett. bioRxiv posted 19 May 2019

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

December 19, 2018

Toady’s digest features research that gives insight on the formation of lower respiratory tract microbiota in infants and the differential role of TL1A in acute and chronic colitis.

General microbiome

Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease – Steven A. Cowman – PLOS ONE


Pregnancy and early life

*Early-Life Formation of the Microbial and Immunological Environment of the Human Airways – CélinePattaroni – Cell Host & Microbe


Human reproductive microbiome

Review: Uterine microbiome—low biomass and high expectations – Iolanda Garcia-Grau – Biology of Reproduction


Human respiratory microbiome

Review: Microbiome and disease in the upper airway – Jivianne T. Lee – Current Opinion in Allergy and Clinical Immunology


Human gut microbiome

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa – Cormac Brian Fitzgerald – BMC Genomics

Retrospective analysis of long-term gastrointestinal symptoms after Clostridium difficile infection in a nonelderly cohort – Tamar F. Barlam – PLOS ONE

Review: Gut microbiota: a potential manipulator for host adipose tissue and energy metabolism – Bohan Rong – The Journal of Nutritional Biochemistry


Animal experiments

*Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis – Jim G.Castellanos – Immunity

LC–MS-Based Metabolomics and Lipidomics Study of High-Density-Lipoprotein-Modulated Glucose Metabolism with an apoA-I Knockout Mouse Model – Jia Liu – Journal of Proteome Research

TLR4 deficiency reduces pulmonary resistance to Streptococcus pneumoniae in gut microbiota-disrupted mice – Hongyan Wang – PLOS ONE

Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats – Deliang Liu – Biomedicine & Pharmacotherapy


Animal microbiome

Floral and Foliar Source Affect the Bee Nest Microbial Community – Jason A. Rothman – Microbial Ecology

Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus – Matthew Fuirst – PLOS ONE

Disruption of the microbiota affects physiological and evolutionary aspects of insecticide resistance in the German cockroach, an important urban pest – Jose E. Pietri _ PLOS ONE

The composition and structure of the intestinal microflora of Anguilla marmorata at different growth rates: a deep sequencing study – Mao Lin – Journal of Applied Microbiology

Review: Composition and functional roles of the gut microbiota in mosquitoes – Michael R. Strand – Current Opinion in Insect Science

Review: Transcriptomic analyses uncover emerging roles of mucins, lysosome/secretory addressing and detoxification pathways in insect midguts – Walter R. Terra – Current Opinion in Insect Science

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals – Amanda C. Perofsky – The ISME Journal


Plant, root, and soil microbiome

Dead or alive; or does it really matter? Level of congruency between trophic modes in total and active fungal communities in High Arctic soil – Magdalena Wutkowska – Frontiers in Microbiology


Water and extremophile microbiome

Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities – Alberto Scoma- The ISME Journal

Evidence of selective pressure in whale fall microbiome proteins and its potential application to industry – Robert Cardoso deFreitas – Marine Genomics

AgNPs change microbial community structures of wastewater – Yuting Guo – Frontiers in Microbiology

Performance and microbial community of an electric biological integration reactor (EBIR) for treatment of wastewater containing ibuprofen – Yan Feng – Bioresource Technology

 

Food microbiology

Spoilage microbial community profiling by 16S rRNA amplicon sequencing of modified atmosphere packaged live mussels at cold storage temperature – Olumide A.Odeyemi – Food Research International

Genomic resolution of bacterial populations in saccharin and cyclamate degradation – YuDeng – Science of The Total Environment


Phages and viruses

Nanopore-based detection and characterization of yam viruses – Denis Filloux – Scientific Reports


Metabolomics

Active Acupoints Differ from Inactive Acupoints in Modulating Key Plasmatic Metabolites of Hypertension: A Targeted Metabolomics Study – Mingxiao Yang – Scientific Reports


Techniques

Review: Quantifying microbial chatter: scanning electrochemical microscopy as a tool to study interactions in biofilms – Sophie E. Darch – Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences

Metabolic Fingerprinting of Bacteria Exposed to Nanomaterials, Using Online Databases, NMR, and High-Resolution Mass Spectrometry – Theodoros G. Chatzimitakos – Nanotoxicity

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Science, publishing, and career

Commentary : Communicating health risks in science publications: time for everyone to take responsibility – Alexandra L. J. Freeman – BMC Medicine

Could a double blind peer review process reduce gender bias?

Preprint: The Case For and Against Double-blind Reviews – Amelia R – bioRxiv

November 30, 2018

Happy Friday! Today’s digest features the skin microbiome of lizards and frogs, bacterial changes during palm wine fermentation, and the impact of deforestation on soils in the Amazon.

General microbiome

Review: The microbiome in threatened species conservation – West – Biological Conservation

Human oral microbiome

Oxidative stress in the oral cavity is driven by individual-specific bacterial communities – Džunková – NPJ Biofilms and Microbiomes

Human gut microbiome

Alterations of the gut microbiome and plasma proteome in Chinese patients with adolescent idiopathic scoliosis – Shen – Bone

Animal experiments

Effect of gastric fluid aspiration on the lung microbiota of laboratory rats – Finn – Experimental Lung Research

Animal microbiome

Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia – Weitzman – PeerJ

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets – Poulsen – PLoS One

Plant, root, and soil microbiome

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis – Zhu – Environmental Science and Technology

Deforestation Impacts Network Co-occurrence Patterns of Microbial Communities in Amazon Soils – Khan – FEMS Microbiology Ecology

Review: VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes – Tyagi – Critical Reviews in Biotechnology

Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard – Liang – Microbiological Research

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential – Martins – Microbiome

Extemophile microbiome

Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities – Kalwasińska – Science of the Total Environment

Food microbiology

Preprint: Bacterial diversity and population dynamics during the fermentation of palm wine from Guerrero Mexico – Astudillo-Melgar – BioRxiv

Assessment of biogas production and microbial ecology in a high solid anaerobic digestion of major California food processing residues – Achmon – Bioresource Technology Reports

Science, publishing, and career

Preprint: Participation and Motivations of Grant Peer Reviewers: A Comprehensive Survey of the Biomedical Research Community – Gallo – BioRxiv

October 24, 2018

General Microbiome

REVIEW:Leaky Gut, Leaky Brain? Obrenovich MEM. Microorganisms.

Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children.Chen B. International Immunopharmacology.

Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure.Wang L. Ecotoxicology and Environmental Safety

Gut Microbiome

Association of serum bilirubin in newborns affected by jaundice with gut microbiota dysbiosis.Zhou S. The Journal of Nutritional Biochemistry

Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Zhernakova DV. Nature Genetics

Competitive lottery-based assembly of selected clades in the human gut microbiome.Verster AJ. Microbiome.

Vaginal Microbiome

Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study.Arokiyaraj S. Scientific Reports

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis.Boyer E. Scientific Reports

Plant, Soil, and Water Microbiome

Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers.He Z. Environmental Pollution

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters.Deja-Sikora E. Microbial Ecology

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales.Li HY. Microbiome

Potential methane production and molecular characterization of bacterial and archaeal communities in a horizontal subsurface flow constructed wetland under cold and warm seasons. López D. The Science of the Total Environments

Biotechnological potential of plant growth-promoting bacteria from the roots and rhizospheres of endemic plants in ironstone vegetation in southeastern Brazil.Felestrino ÉB. World Journal of Microbiology and Biotechnology

Temporal shifts in endophyte bacterial community composition of sessile oak (<i>Quercus petraea</i>) are linked to foliar nitrogen, stomatal length, and herbivory. Borruso L. Peer

Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting <i>Mussaenda shikokiana</i> along an elevation gradient.Qian X. PeerJ.

Techniques

Protocol for faecal microbiota transplantation in ulcerative colitis (FMTUC): a randomised feasibility study.Jitsumura M. BMJ Open

September 20, 2018

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

General microbiome

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

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

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

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

Pregnancy and early life

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

Human gut microbiome

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

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

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

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

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

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

Animal experiments

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

Water and extremophile microbiome

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

Probiotics/Prebiotics

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

Microbes in the news

The case for expensive antibioticshttp://www.wired.com

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

Non-microbiology picks

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