Category Archives: Animal experiments

July 31, 2020

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Today’s digest features studies on hospital-associated bacterial communities on window components, the effect of urbanization on the vaginal microbiota of Amerindians, nitrate as a potential prebiotic for oral health, and the latest news in bioinformatics. Happy reading!

General microbiome

Microbial species interactions determine community diversity in fluctuating environments – Shota Shibasaki – bioRxiv

Review: The host-associated archaeome – Guillaume Borrel – Nature Reviews Microbiology

Oral microbiome

*Nitrate as a potential prebiotic for the oral microbiome – Bob T. Rosier – Scientific Reports

Skin microbiome

Deep skin dysbiosis in vitiligo patients: link with mitochondrial and immune changes – Hanene Bzioueche – medRxiv

Gut microbiome

Review: The microbiome: An emerging key player in aging and longevity– Minhoo Kim and Bérénice A. Benayoun – Translational Medicine of Aging

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Kelsey E. Huus – Microbiome

Vaginal microbiome

*Changes in the vaginal microbiota across a gradient of urbanization – Daniela Vargas-Robles – Scientific Reports

Comparison between a novel molecular tool and conventional methods for diagnostic classification of bacterial vaginosis: is integration of the two approaches necessary for a better evaluation? – Margherita Scapaticci – New Microbiologica

Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence – Norhan Alhajjar – bioRxiv

Association between Vaginal Bacterial Microbiota and Vaginal Yeast Colonization – McKenna C Eastment – The Journal of Infectious Diseases

Urinary microbiome

Review: The microbiome in urological diseases – Kwang Woo Lee – Investigive and Clinical Urology

Review: FimH and Anti-Adhesive Therapeutics: A Disarming Strategy Against Uropathogens – Meysam Sarshar – Antibiotics

Characterization of urinary microbiome in patients with bladder cancer: Results from a single-institution, feasibility study – Juan Chipollini – Urologic Oncology: Seminars and Original Investigations

Animal microbiome

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage – Jolinda Pollock – Scientific Reports

Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers – Juan J. Quereda – Frontiers in Veterinary Science

Animal experiment

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Eliran Kadosh – Nature

An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut – Gustavo Caballero-Flores – Cell Host & Microbe

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin – Damien J. Cabral – mSystems

Water and extremophile microbiome

Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer – Jessica Hinojosa – Water Research

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities – Tyler J. Arbour – Frontiers in Microbiology

Food microbiome

Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring – Luca Belleggia – Food Microbiology

Built environment

*Viable bacterial communities on hospital window components in patient rooms – Patrick F. Horve – PeerJ

Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation – Ganesh Babu Malli Mohan – mSystems

Phages and viruses

Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone – Anastasia Tsiola – Viruses

Bioinformatics

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets – Yi Yue – BMC Bioinformatics

Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach – Christian Milani – mSystems

Automated prediction and annotation of small proteins in microbial genomes– Matthew G Durrant and Ami S Bhatt – bioRxiv

Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data – Abigail L. Lind – bioRxiv

MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline – Carlos A. Ruiz-Perez – bioRxiv

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra – Caroline Weis – Bioinformatics

NetCoMi: Network Construction and Comparison for Microbiome Data in R – Stefanie Peschel – bioRxiv

Review: Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses – Ana Elena Pérez-Cobas – Microbial Genomics

Podcast

Machine learning for drug development with Marinka Zitnik – Jacob Schreiber – The Bioinformatics Chat

July 27, 2020

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Greetings from Pittsburgh!

Saturday and Sunday’s digests were packed full of great articles, which means the week is off to a slower start than usual. We’ve got two environmentally focused preprints that I am super excited about, a paper demonstrating how microbiota can be dosed in order to help mice mitigate intestinal cancer and inflammation, and a paper focused on the eco-thermodynamics of methanogenic bioprocesses. Enjoy!

Animal experiments

Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis – Zhang et al. – Microbiome

Water and extremophile microbiome

Preprint: Distinct microbial communities along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents – Somee et al. – BioRxiv

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses – Nobu et al. – Microbiome

Preprint: Freshwater monitoring by nanopore sequencing – Urban et al. – bioRxiv

July 25, 2020

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Good morning and happy Saturday y’all! Today’s digest is brief, but covers some fascinating papers including: small RNAs regulating gut microbe metabolism; epigenetics linking the early-life airway microbiota with allergic rhinitis; and the impact of gut microbial composition on vagal innervation. I’ve also included a non-microbiome pick discussing how to spot and resolve common statistical mistakes in research manuscripts. The authors of the article hope this will help improve robustness of scientific research. Happy reading!

Gut Microbiome
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron. Ryan, D. et al. Nature Communications.

Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19. Zuo, T. et al. Gut.

High microbiota reactivity of adult human intestinal IgA requires somatic mutations. Kabbert, J. et al. Journal of Experimental Medicine.

A unified catalog of 204,938 reference genomes from the human gut microbiome. Almeida, A. et al. Nature Biotechnology.

Airway Microbiome
Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age. Morin, A. et al. Journal of Allergy and Clinical Immunology.

Early-Life Microbiome
Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways. Pichler, M.J. et al. Nature Communications.

Animal Experiments
Bile acids drive the newborn’s gut microbiota maturation. van Best, N. et al. Nature Communications.

Gut microbiota composition modulates inflammation and structure of the vagal afferent pathway. Kim, J.S. et al. Physiology & Behavior.

TNFα regulates intestinal organoids from mice with both defined and conventional microbiota. Sun, L. et al. International Journal of Biological Macromolecules.

Water Microbiome
Nutrient and microbial water quality of the upper Ganga River, India: identification of pollution sources. Bowed, M.J. et al. Environmental Monitoring and Assessment.

Plant, Root, and Soil Microbiome
Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment. Aydogan, E.L. FEMS Microbiology and Ecology.

Non-Microbiome Pick
Science Forum: Ten common statistical mistakes to watch out for when writing or reviewing a manuscript. Makin, T.R. and Orban de Xivry, JJ. eLife.

July 23, 2020

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In today’s digest – duodenal microbiota linked to stunting in children, differential effects of germfree and antibiotic treated mouse models on social behavior, microbial metabolite receptor GPBAR and its interaction with bile acids, review article on engineering microbes to treat diseases and many more…happy reading!

General microbiome

The Microbiota-Gut-Immune-Glia (MGIG) Axis in Major Depression – Leszek Rudzki – Molecular Neurobiology

Engineering the gut microbiota to treat chronic diseases – Noura S. Dosoky – Applied Microbiology and Biotechnology

Human microbiome

Acute and chronic improvement in postprandial glucose metabolism by a diet resembling the traditional Mediterranean dietary pattern: Can SCFAs play a role? – Marilena Vitale – Clinical Nutrition

Linking the duodenal microbiota to stunting in a cohort of undernourished Bangladeshi children with enteropathy – Robert Y. Chen – New England Journal of Medicine

Enterobacterales Infection after Intestinal Dominance in Hospitalized Patients – Krishna Rao – mSphere

Differences in the gut Firmicutes to Bacteroidetes ratio across age groups in healthy Ukrainian population – Alexander Vaiserman – BMC Microbiology

Preprint- Association of gut microbiota with cerebral cortex and cerebrovascular abnormality in human mild traumatic brain injury – Lijun Bai – BioRxiv

Real-world study in infants fed an infant formula with two human milk oligosaccharides – Enriqueta Román – Nutricion Hospitalaria

Animal experiments

Gut microbiome composition differences among breeds impact feed efficiency in swine – Matteo Bergamaschi – Microbiome

Opposing effects of antibiotics and germ-free status on neuropeptide systems involved in social behaviour and pain regulation – Katerina V. A. Johnson – BMC Neuroscience

Local Necrotic Cells Trigger Systemic Immune Activation via Gut Microbiome Dysbiosis in Drosophila – Hina Kosakamoto – Cell Reports

Peanut skin extract ameliorates the symptoms of type 2 diabetes mellitus in mice by alleviating inflammation and maintaining gut microbiota homeostasis – Lan Xiang – Aging

Preprint- Community composition and development of the post-weaning piglet gut microbiome – D. Gaio – BioRxiv

Gut microbiota regulate tumor metastasis via circRNA/miRNA networks – Zhuxian Zhua – Gut Microbes

Porcine circovirus type 2 (PCV2) and Campylobacter infection induce diarrhea in piglets: Microbial dysbiosis and intestinal disorder – Gang Yang – Animal Nutrition

Plant, root and soil microbiome

Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota – Sarah Huet – Frontiers in Plant Science

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat – Aymé Spor – Scientific Reports

Water microbiome

Preprint- Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs – A. Meziti – BioRxiv

Preprint- Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing – Kimothy L. Smith – BioRxiv

Phages and Viruses

Preprint- Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract – Sabrina I. Green – BioRxiv

Techniques
Structural basis of GPBAR activation and bile acid recognition – Fan Yang – Nature

Microbes in News

Machine learning analysis reveals less diverse microbiome in children with type 1 diabetes – Healio

July 15, 2020

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There are several notable entries in today’s digest. Registration is open for the European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” virtual training course. The course is for European secondary school science teachers and is 5 weeks long. The 3rd Microbiome Movement will also be held this year, both virtually and in-person. Links are in the Events section.  

Today I’ve highlighted a bioinformatics paper on variant calling for cpn60 barcode sequencing and an early life paper on pre-term infant stem cell proliferation upregulated by microbial metabolites. While putting this digest together, I learned algae turns snow different colors! This is so cool to me that I’ve highlighted that paper as well. Finally, the News section includes an article for Smithsonian Magazine by Rob Dunn on quarantine’s effects on our microbial passengers.  

Happy reading!

Events

3rd Microbiome Movement – Animal Health & Nutrition Summit, taking place in North Carolina as well as digitally October 19-21, 2020.

European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” November 2-December 7, 2020. Applications are due October 15 and the course is free.

Pregnancy and early life

Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites – Michael W. Dougherty – BMC Microbiology

Human gut microbiome

Perspective: Gut microbiome, big data and machine learning to promote precision medicine for cancer – Giovanni Cammarota – Nature Reviews Gastroenterology & Hepatology

Microbiome of death

Characterizing the postmortem human bone microbiome from surface-decomposed remains – Alexandra L. Emmons – PloS One

Animal experiments

Saccharomyces cerevisiae fermentation products (SCFP) stabilize the ruminal microbiota of lactating dairy cows during periods of a depressed rumen pH – Hein M. Tun – BMC Veterinary Research

Animal microbiome

A Shift Pattern of Bacterial Communities Across the Life Stages of the Citrus Red Mite, Panonychus citri – Zhen-yu Zhang – Frontiers in Microbiology

Plant, root, and soil microbiome

Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses – Mary Donato – PloS One

Bioavailable metal (loid) s and physicochemical features co-mediating microbial communities at combined metal (loid) pollution sites – Jiawen Wang – Chemosphere

Assessing the effects of tylosin fermentation dregs as soil amendment on macrolide antibiotic resistance genes and microbial communities: Incubation study – Bo Zhang – Journal of Environmental Science and Health, Part B

Book: Phytobiomes: Current Insights and Future Vistas – Manoj Kumar Solanki – Springer

Early changes in bacterial communities in wound tissues of Pinus massoniana after inoculation with Bursaphelenchus xylophilus – Jinyan Liu – Nematology

Preprint: Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil – Alexa M. Nicolas – bioRxiv

Preprint: A Meta-analysis of the known Global Distribution and Host Range of the Ralstonia Species Complex – Tiffany Lowe-Power – bioRxiv

Water, air, and extremophile microbiome

Lipid Biomarker Record of the Serpentinite-Hosted Ecosystem of the Samail Ophiolite, Oman and Implications for the Search for Biosignatures on Mars – Sharon A Newman – Astrobiology

Metabolic acclimation of anammox consortia to decreased temperature – Tangran Huo – Environment International

Complete Genome Sequences of Two Marine Biofilm Isolates, Leisingera sp. nov. Strains 201A and 204H, Novel Representatives of the Roseobacter Group – Giselle S. Cavalcanti – Microbiology Resource Announcements

Microbial interspecific interaction and nitrogen metabolism pathway for the treatment of municipal wastewater by iron carbon based constructed wetland – Xiao Huang – Bioresource Technology

Biogeographical distribution of dissimilatory nitrate reduction to ammonium (DNRA) bacteria in wetland ecosystems around the world – Huawei Pan – Journal of Soils and Sediments

Molecular diversity of the microbial community in coloured snow from the Fildes Peninsula (King George Island, Maritime Antarctica) – Wei Luo – Polar Biology

Novel arsenic hyper-resistant bacteria from an extreme environment, Crven Dol mine, Allchar, North Macedonia – Vladimir Bermanec – Journal of Hazardous Materials

Built environment

Ozone treatment in a wind tunnel for the reduction of airborne viruses in swine buildings – Jonathan M. Vyskocil – Aerosol Science and Technology

Food microbiology

Correlation between microbial communities and key flavors during post-fermentation of Pixian broad bean paste – Ping Liu – Food Research International

Additives affect the distribution of metabolic profile, microbial communities and antibiotic resistance genes in high-moisture sweet corn kernel silage – Zhe Wu – Bioresource Technology

Shifts in autochthonous microbial diversity and volatile metabolites during the fermentation of chili pepper (Capsicum frutescens L.) – Xinxing Xu – Food Chemistry

Proteomic characterization of extracellular vesicles produced by several wine yeast species – Ana Mencher – Microbioal Biotechnology

Book Chapter: Role of Microbes for Attaining Enhanced Food Crop Production – Pankaj Sharma – Microbial Biotechnology: Basic Research and Applications

Bioinformatics

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling – Sarah J. Vancuren – PloS One

Techniques

Preprint: Visualization of giant virus particles using BONCAT labeling and STED microscopy – Monica Berjon-Otero – bioRxiv

Microbes in the News

Human Microbiome: 39 trillion microbes and bacteria that call us home – Mun-Keat Looi – Science Focus

What Quarantine is Doing to Your Body’s Wondrous World of Bacteria – Rob Dunn – Smithsonian Magazine

July 13, 2020

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Greetings from Pittsburgh, PA!

Included is a wide range of microbial ecology articles focused on everything from the human microbiome to soil microbial fuel cells. I want to give a special highlight to the article about how the indoor microbial community changes in response to bed bug infestations. This study incorporates a few of my favorite disciplines including entomology, public health, the built environment, as well as microbiology. If you’re interested in learning more about bed bugs, I’ll also recommend one my favorite reads from a few years ago: Infested: How the bed bug infiltrated our bedrooms and took over the world by Brooke Borel.

Events and jobs

In my last microbiome digest, I gave a special plug for the National Summer Undergraduate Research Project (NSURP). NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC undergraduate students in the microbial sciences. They have already paired over 140 students with summer research opportunities, but they still need mentors for remaining student applicants. Please apply and share widely!

General microbiome

The beta-diversity of Siganus fuscescens-associated microbial communities from different habitats increases with body weight – Wu et al. – Frontiers in Microbiology

Human gut microbiome

Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut – Chng et al. – Nature Ecology & Evolution

The gut microbiome during acute lifestyle transition – Devkota – Nature Medicine

Review: Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology – Wian and Ho – Biophysical Reviews

Animal experiments

The gut and feed residue microbiota changing during the rearing of Hermetia illucens larvae – Cifuentes et al. – Antonie van Leeuwenhoek

Animal microbiome

Effect of introduced parasites on the survival and microbiota of nestling cactus finches (Geospiza scandens) in the Galápagos Islands – Addesso et al. – Journal of Ornithology

Direct comparison of fecal and gut microbiota in the Blue Mussel (Mytilus edulis) discourages fecal sampling as a proxy for resident gut community – Griffin et al. – Microbial Ecology

Plant, root, and soil microbiome

Variable microbial communities in the non-hydrothermal sediments of the Mid-Okinawa trough – Cao et al. – Geomicrobiology Journal

Review: Microbial communities from arid environments on a global scale. A systematic review – Vásquez-Dean et al. – Biological Research

Unravelling metabolism and microbial community of a phytobed co-planted with Typha angustifolia and Ipomoea aquatica for biodegradation of doxylamine from wastewater – Xiong et al. – Journal of Hazardous Materials

Built environment

Bed bugs shape the indoor microbial community composition of infested homes – Kakumanu et al. – Science of the Total Environment

Effect of sono-thermal pre-treatment over methane production, specific activities and the microbial community of sludge anaerobic digesters – Neumann et al. – Waste and Biomass Valorization

Effects of anode materials on the performance and anode microbial community of soil microbial fuel cell – Yu et al. – Journal of Hazardous Material

Techniques

Review: Targeted microbiome depletion – Du Toit – Nature Reviews Microbiology

July 10, 2020

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Today’s digest contains many exciting articles – gut microbiome in precision medicine for cancer, important review on patent protection in microbiome therapeutics, role of the gut microbiota in sympathetic neurons, interaction of pacemaker neurons with the gut microbiota, gut dysbiosis in lupus and many more….Enjoy reading and happy weekend!

General microbiome

Gut microbiome, big data and machine learning to promote precision medicine for cancer – Giovanni Cammarota – Nature Reviews Gastroenterology and Hepatology

Co-evolution and Co-speciation of Host-Gut Bacteria Systems – Mathieu Groussin – Cell Host and Microbe

Microbiome therapeutics and patent protection – Mark J. FitzGerald – Nature Biotechnology

Human microbiome

Fecal Microbiota Transplantation is Safe and Effective in Patients with Clostridioides difficile Infection and Cirrhosis – Yao-WenCheng – CLinial Gastroenterology and Hepatology

Association of Gut Microbiota-Dependent Metabolite Trimethylamine N-Oxide with First Ischemic Stroke – Taoping Sun – Journal of Atherosclerosis and Thrombosis

Dietary Strategies for Maintenance of Clinical Remission in Inflammatory Bowel Diseases: Are We There Yet? – Konstantinos Gkikas – Nutrients

The duodenal microbiome is altered in small intestinal bacterial overgrowth – Gabriela Leite – PlosOne

Faecal microbiota transplantation: A life-saving therapy challenged by commercial claims for exclusivity – Christian LodbergHvas – EClinical Medicine

Animal experiments

Microbiota modulate sympathetic neurons via a gut–brain circuit – Paul A. Muller – Nature

Prototypical pacemaker neurons interact with the resident microbiota – Alexander Klimovich – PNAS

Gut microbiota dysbiosis and altered tryptophan catabolism contribute to autoimmunity in lupus-susceptible mice – Seung-Chul Choi – Science Translational Medicine

The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease – Yu Liu – Faseb Journal

Sodium Butyrate Alleviates Mouse Colitis by Regulating Gut Microbiota Dysbiosis – Xiujing Dou – Animals

Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome – Min-Ting Lee – Journal of Lipid Research

Commentary: Modulating microbiome metabolites in vivo – Chun-Jun Guo – Science

Plant, root and soil microbiome

Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history – Martinus Schneijderberg – ISME Journal

Water microbiome

Anthropogenic dissolved organic carbon and marine microbiomes – Maria Vila-Costa – ISME Journal

Functional foods

Effect of a functional fibre supplement on glycemic control when added to a year-long medically supervised weight management program in adults with type 2 diabetes – Raylene A. Reimer – European Journal of Clinical Nutrition

Prenatal exposure to the probiotic Lactococcus lactis decreases anxiety-like behavior and modulates cortical cytoarchitecture in a sex specific manner – Natalia Surzenko – PlosOne

Non microbiology picks

SARS-CoV-2 is transmitted via contact and via the air between ferrets – Mathilde Richard – Nature Communications

July 8, 2020

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Good morning! Today’s digest includes a broad selection of interesting research. Particular highlights include a study in rats that found microbiota transplantation attenuated neuroinflammation, a human study on the dramatic microbiome effects of dietary glycans, and a new technique for using drones to collect dolphin microbiome samples.

Pregnancy and early life

History of breastfeeding but not mode of delivery shapes the gut microbiome in childhood, Camille C. Cioffi et al., PLOS ONE

Preprint: Gut microbiota and fecal short-chain fatty acids are not associated with bone mass in healthy Chinese children: a cross-sectional study, Fengyan Chen et al., Research Square

Impact of Long-Term and Low-Dose Antibiotic Prophylaxis on Gut Microbiota in Children, Yuko Akagawa et al., The Journal of Urology

Human gut microbiome

Microbiome and health implications for ethnic minorities after enforced lifestyle changes, David M. Keohane et al., Nature Medicine

Preprint: Metaproteomics reveals potential signatures of disease-specific alterations in the gut microbial proteolytic events in inflammatory bowel disease, Zhixiang Yan et al., Research Square

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans, Richard Creswell et al., Genome Medicine

Preprint: High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota, Andres Aranda-Diaz et al., bioRxiv

Preprint: pH-dependent spontaneous hydrolysis rather than gut bacterial metabolism reduces levels of the ADHD treatment, Methylphenidate, Julia Aresti et al., bioRxiv

Animal experiments

The gut microbiota attenuate neuroinflammation in manganese exposure by inhibiting cerebral NLRP3 inflammasome, Wang and Yang et al., Biomedicine & Pharmacotherapy

Magnetic fields modulate metabolism and gut microbiome in correlation with Pgc‐1α expression: Follow‐up to an in vitro magnetic mitohormetic study, Yee Kit Tai et al., The FASEB Journal

Preprint: Multi-omics analysis of aspirin treatment response in mice provide molecular insights and targets linked to liver fibrosis regression, Adil Bhat et al., bioRxiv

Animal microbiome

Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes, Josephine Hyde et al., Scientific Reports

The gut bacterial microbiota of sea turtles differs between geographically distinct populations, T. Franciscus Scheelings et al., Endangered Species Research

Bioinformatics

Sparse reduced-rank regression for integrating omics data, Hilafu, Safo and Haine, BMC Bioinformatics

Techniques

An ecological framework to understand the efficacy of fecal microbiota transplantation, Yandong Xiao et al., Nature Communications

The use of Unmanned Aerial Vehicles (UAVs) to sample the blow microbiome of small cetaceans, Cinzia Centelleghe et al., PLOS ONE

July 4, 2020

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Greetings from Santiago, Chile! Today in this Digest, we have studies about the influence of alcohol use disorder on the microbiota, several papers about the influence of different compounds (from allicin to DAV132, a colon-targeted antibiotic adsorbent) on the microbiota. Today we have several papers about different models of plant- or soil- associated microbiomes, and a couple of papers from studies with SIV infection models. Have a nice weekend!

Human and General Microbiome

Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity – Nancy Ames et al., – Gut Microbes

Comparative evaluation of peptidome and microbiota in different types of saliva samples – Ce Zhu et al., – Annals of Translational Medicine

Preprint: Microbial control over host diet selection – Brian K Trevelline and Kevin D Kohl – BioRxiv

Functional Compounds and the Microbiome

Hemolysin BL from novel Bacillus toyonensis BV-17 induces antitumor activity both in vitro and in vivo – Jiajia Chen et al., – Gut Microbes

Modeling the effect of DAV132, a novel colon-targeted adsorbent, on fecal concentrations of moxifloxacin and gut microbiota diversity in healthy volunteers – Jinju Guk et al., – Clinical Pharmacology and Therapeutics

Allicin-induced host-gut microbe interactions improves energy homeostasis – Chuanhai Zhang et al., – The FASEB Journal

Evidence of Microbiome-Drug Interactions between the Antimalarial Lumefantrine and Gut Microbiota in Mice – Matthew M. Ippolito et al., – The American Society of Tropical Medicine and Hygiene

Contrasting effects of viscous and particulate fibers on colonic fermentation in vitro and in vivo, and their impact on intestinal water studied by MRI in a randomized trial – David Gunn et al., – The American Journal of Clinical Nutrition

Animal Microbiome / Animal Models

A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques – Wendy Li and Zhanshan (Sam) Ma – FEMS Microbiology Ecology

Impact of Initial Feeding and Molting on Tachypleus tridentatus Gut Microbiota – Fengze Miao et al., – Current Microbiology 

Osmotic stress induces gut microbiota community shift in fish – Keng Po Lai et al., – Environmental Microbiology

The Gut-Eye Axis: Lessons Learned from Murine Models – Jason L. Floyd & Maria B. Grant – Ophthalmology and Therapy 

The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage – Kristina Allers et al., – Scientific Reports  

Plant or Soil Microbiomes

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition – Seok-Won Jang et al, – Rice 

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations – Ryan S. McClure et al., – Scientific Reports 

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest – Laura M. Mason et al.,– Journal of Applied Microbiology

Phylogenetic signals and predictability in plant-soil feedbacks – Elizabeth M. Wandrag et al., – New Phytologist

Genomics / Bioinformatics

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites – Feifei Xu et al., – Microbial Genomics 

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey et al., – Genome Research

Other papers

Preprint: Metagenome-assembled genomes from Monte Cristo Cave (Diamantina, Brazil) reveal prokaryotic lineages as functional models for life on Mars – Amanda G Bendia et al., – BioRxiv 

Preprint: Exploring metal resistance genes and mechanisms in copper enriched metal ore metagenome – Esmaeil Forouzan Sr. et al., – BioRxiv

SARS-CoV-2 Preprints

Preprint: Alpha-1 antitrypsin inhibits SARS-CoV-2 infection – Lukas Wettstein et al., – BioRxiv

June 23, 2020

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Human gut microbiome

US nativity and dietary acculturation impact the gut microbiome in a diverse US population – Peters et al. – The ISME Journal


GlycA, a novel marker for low grade inflammation, reflects gut microbiome diversity and is more accurate than high sensitive CRP in reflecting metabolomic profile – Mokkala et al. – Metabolomics

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Black tea benefits short‐chain fatty acid producers but inhibits genus Lactobacillus in the gut of healthy Sprague–Dawley rats – Gao et al. – Journal of the Science of Food and Agriculture

Animal microbiome (for animals in the wild)

A role for gut microbiota in host niche differentiation – Greene et al. – The ISME Journal


Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species – Li – The ISME Journal

Plant, root, and soil microbiome

Recovery of fen peatland microbiomes and predicted functional profiles after rewetting – Emsens – The IMSE Journal
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments – Zhang et. al – Microbiome

Antibiotic resistance

Chlorine disinfection promotes the exchange of antibiotic resistance genes across bacterial genera by natural transformation – Jin et al. – The ISME Journal

Phages and viruses

Narnaviruses: novel players in fungal–bacterial symbioses – Espino-Vazquez – The ISME Journal