August 26, 2020

Posted on August 26, 2020 by barakdror

Shalom from Israel! Today’s digest has some great review papers, as well as research articles focusing on citures disease, vaginal microbiome, gut virome and some cool bioinformatic tools.

Also, check out this great event for the soil microbilogists out there: Non-academic Careers in Soil Ecology: a virtual career panel, hosted by MSU.

Enjoy your summer holiday if you managed to get one and as always- find yourself the time to rest and re-energize.

General

**review: Compartmentalization drives the evolution of symbiotic cooperation, Guillaume Chomicki, Phil. Tran. B

Marine microbiomoe

Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef, Carmen Astudillo-Garica , Env. Micro.

Plant microbiome

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome, Bridget L. Hansen , mBio

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil, Evan P. Starr, bioRxiv

Disease-Induced Microbial Shifts in Citrus Indicate Microbiome-Derived Responses to Huanglongbing Across the Disease Severity Spectrum, Nichole A. Ginnan , Phytobiomes

Human microbiome and virome

Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy, Andrew Oliver , mBio

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut, Ann C. Gregory , Cell Host Microbe

Bioinformatics

BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters, Satria Kutsar, bioRxiv

**mini-review: Natural product discovery through microbial genome mining, Emma Kenshole, Cur. Op. Chem. Bio.

Available Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations, Murilo Henrique Anzolini Cassiano, mSystems

June 28, 2020

Posted on June 28, 2020 by jlrobson

Greetings from Wiltshire, England!

Today’s digest brings a little bit of everything. We’ve been cataloguing the latest COVID-19 publications during this pandemic, and today I’m please to bring you a paper combining both COVID-19 and microbiome research!

Elsewhere, there are plenty of environmental microbiome publications, including a great paper on the challenges of studying microbiology in space, an analysis of how aerosols spread COVID-19 and other infectious agents in dental practices, and plenty of articles on various aspects of soil microbiomes.

I hope everyone’s coping well during these times. On a personal level, I’m delighted to be returning to the lab this week to resume my PhD research into gut microbiomes and cancer. I’m glad to be back, but worried about how my pipetting skills have suffered during my time off!

Stay safe, and happy reading!

COVID-19

Intestinal Flora as a Potential Strategy to Fight SARS-CoV-2 Infection – He et al. – Frontiers in Microbiology

Preprint: Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry – Ozono et al.

Human vaginal microbiome

Novel Potential Probiotic Lactobacilli for Prevention and Treatment of Vulvovaginal Infections – Kumherová et al. – Probiotics and Antimicrobial Proteins

Preprint: The structure and diversity of strain level variation in vaginal bacteria –Tortelli et al.

Human gut microbiome

Early exposure to food contaminants reshapes maturation of the human brain-gut-microbiota axis – Sarron et al. – World Journal of Gastroenterology

Luminal microbiota related to Crohn’s disease recurrence after surgery – Hamilton et al. – Gut Microbes

Animal experiments

Preprint: The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet – Mims et al.

Animal microbiome

Germ-free housing conditions do not affect aortic root and aortic arch lesion size of late atherosclerotic low-density lipoprotein receptor-deficient mice – Kiouptsi et al. – Gut Microbes

The effects of environment and ontogeny on the skin microbiome of two Stegastes damselfishes (Pomacentridae) from the eastern Caribbean Sea – Xavier et al. – Marine Biology

Variations and Potential Factors of Gut Prokaryotic Microbiome During Spawning Migration in Coilia nasus – Ying et al. – Current Microbiology

Plant, root, and soil microbiome

Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. – Delamuta et al. – International Journal of Systematic and Evolutionary Microbiology

Efects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil – Salam et al. – Bioresources and Bioprocessing

Differences in soil microbial communities and enzyme activity due to the application of bioslurry under cultivation – Mofokeng et al. – South African Journal of Plant and Soil

Microbial Communities in the Fynbos Region of South Africa: What Happens during Woody Alien Plant Invasions – Jacobs et al. – Diversity

Water and extremophile microbiome

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location – Schulhof et al. – Molecular Ecology

Preprint: Fungal communities in sediments along a depth gradient in the Eastern Tropical Pacific – Rojas-Jimenez et al

Built environment

Preprint: Evaluating aerosol and splatter following dental procedures – Allison et al.

Microbes in space

Current Progression: Application of High-Throughput Sequencing Technique in Space Microbiology – Chen et al. – BioMed Research International

Food microbiology

Swine Methicillin-resistant Staphylococcus aureus carrying toxic-shock syndrome toxin gene in Hong Kong, China – Sapugahawatte et al. – Emerging Microbes and Infections

Probiotics / prebiotics

Moving from probiotics to precision probiotics – Veiga, et al. – Nature Microbiology

Phages and viruses

Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia – Gaccioli et al. – Nature Microbiology

Techniques

Developing standards for the microbiome field – Amos et al. – Microbiome

Microbes in the news

Team Examines Microbiome of Marine Invertebrate That Produces Anticancer Compound – Technology Networks

Bacteria live on our eyeballs — and understanding their role could help treat common eye diseases – Yahoo! News

June 12, 2020

Posted on June 12, 2020 by Jose Gracia

Buenos dias and greetings from Spain!

Today we can announce a Virtual Skin Microbiome Symposium held by New York Society of Cosmetic Chemists (NYSCC), that will start on June 15 to June 22, 2020, will include five on-demand sessions, a live panel Q&A and the Suppliers’ Day Digital Pop-Up & Solutions Center.

COVID-19

Epidemiological models are important tools for guiding COVID-19 interventions – Robin N. Thompson – BMC Medicine

Diagnosis of COVID-19 in children: the story evolves – R. Harwood and I. Sinha – BMC Medicine

Africa’s response to COVID-19 – Chikwe Ihekweazu and Emmanuel Agogo – BMC Medicine

Evaluation of the potential incidence of COVID-19 and effectiveness of containment measures in Spain: a data-driven approach – Alberto Aleta and Yamir Moreno – BMC Medicine

Pre-print – Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype – Shubham Gaurav – bioRxiv

General microbiome

Feasibility of collection and analysis of microbiome data in a longitudinal randomized trial of community gardening – Mireia Gascon – Future microbiology

Targeted microbiome depletion – A Du Toit – Nature Reviews Microbiology

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host D Gouveia et al. – Biofilms and Microbiomes

Microbiome factors in HPV-driven carcinogenesis and cancers D Lin et al. – Plos Pathogens

Human respiratory microbiome

Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia – Heping Wang – PLOS ONE

Human vaginal microbiome

Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis – Anna-Ursula Happel – PLOS ONE

Human nearly-sterile sites

Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov. – Paul A. Lawson et al. – Microbiology society

Draft Genome Sequence of Escherichia coli UMB1353, Isolated from the Female Urinary Tract – T Crawford et al. – Microbiology Resource Announcements

Human gut microbiome

Pre-print – The effect of short-course antibiotics on the resistance pro le of colonizing gut bacteria in the ICU: a prospective cohort study – C Munck et al. – Research Square

Pre-print – Dietary sphinganine is selectively assimilated by members of the gut microbiome – Min-Ting Lee et al. – bioRxiv

Pre-print – Nutritional combinatorial impact on the gut microbiota and plasma short-chain fatty acids levels in the prevention of mammary cancer in Her2/neu estrogen receptor-negative transgenic mice – Manvi Sharma et al. – bioRxiv

Animal experiments

Evaluation of the bacterial ocular surface microbiome in ophthalmologically normal dogs prior to and following treatment with topical neomycin-polymyxin-bacitracin – Callie M Rogers et al. – PLOS ONE

Short-chain fructo-oligosaccharides supplementation to suckling piglets: Assessment of pre- and post-weaning performance and gut health – Miriam Ayuso – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen et al. – PLOS ONE

Effect of dietary gossypol supplement on fermentation characteristics and bacterial diversity in the rumen of sheep – CaiDie Wang – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen – PLOS ONE

β-glucan administration improves growth performance and gut health in New Zealand White and APRI rabbits with different breed responses – Mahmoud M Abo Ghanima – PLOS ONE

Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau – H Liu, X Zhao – PeerJ

Pre-print – Differential genes and microbiota revealed by serum metabolomics of obese rats after intervention by Rhizoma Coptidis – K Luo et al. – Research Square

Pre-print – Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria – Leeann Klassen et al. – bioRxiv

Animal microbiome

Characterizing the microbiome of ectoparasitic louse flies feeding on migratory raptors – Rebecca A McCabe et al. – PLOS ONE

Characterization of the microbiota of commercially-traded finfish fillets – HR Shehata et al. – Food Research International

A bug’s life-delving into the challenges of helminth microbiome studies – F Formenti et al. – PLoS Neglected Tropical Diseases

Fish skin and gut microbiomes show contrasting signatures of host species and habitat – FÉ Sylvain et al. – Applied and Environmental

Plant, root, and soil microbiome

Isolation, Screening and Identification of Free-Living Diazotrophic Bacteria from Salinated Arid Soils – SA Begmatova et al. – Microbiology

Eukaryotic Microbial Communities in Japanese Arable AndisolsInvestigated by Amplicon Sequencing of 18S rRNA – GenesKazumori Mise et al. – American Society for microbiology

Combined effects of green manure returning and addition of sewage sludge compost on plant growth and microorganism communities in gold tailings. – YJ Ai et al. – Environmental Science and Pollution

Taxonomic shifts in arbuscular mycorrhizal fungal communities with shade and soil nitrogen across conventionally managed and organic coffee agroecosystems. – L Aldrich-Wolfe et al. – Mycorrhiza

Metagenomics Framework for the study of Soil Microbial Communities Based 16s rRNA Gene profiling approach – A Basu et al. – International Journal of Biotechnology

Soil microbial communities in the rhizosphere of Robinia pseudoacacia L. after being exposed to elevated atmospheric CO2 and cadmium for 4 years – X Jia et al. – Applied Soil Ecology

Soil aggregates by design: Manufactured aggregates with defined microbial composition for interrogating microbial activities in soil microhabitats – HJ Harvey et al – Soil Biology and Biochemistry

Would fertilization history render the soil microbial communities and their activities more resistant to rainfall fluctuations? J Kátai et al. – biorxiv

Pre-print – Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae – Justine Charon et al. – bioRxiv

Water and extremophile microbiome

Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area – Shuping Wang et al. – PLOS ONE

Spatial dynamics of eukaryotic microbial communities in the German Bight – PAA Sprong et al. – Journal of Sea Research

Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods – H Barak et al. – Chemosphere

Pre-print – Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers – Chenjing Jiang et al. – bioRxiv

Pre-print – Ozone nanobubble treatment effectively reduced pathogenic Gram positive and negative bacteria in freshwater and safe for tilapia – Chayuda Jhunkeaw et al. – bioRxiv

Pre-print – Impact of trimethoprim on the river microbiome and antimicrobial resistance. James Delaney et al. – bioRxiv

Bioinformatics

gutMEGA: a database of the human gut MEtaGenome Atlas – Q Zhang et al. – Briefings in Bioinformatics

June 09, 2020

Posted on June 9, 2020 by barakdror

Good morning everyone!

Today’s digest presents several antibiotic resistance papers, as well as hospital ICU microbiome study, a microbial nomenculture paper, bunch of human microbiome papers (both gut and vaginal), as well as two computational platforms for analyzing microbial data.

In a more personal note– recently, my PhD research (at ARO and The Hebrew U, Israel) resulted in two manuscripts dealing with the exciting world of bacterial secondary metabolites. The first one is a review paper where we present state-of-the-art tools and methodologies to study and identify novel secondary metabolites gene clusters within the widely diverse soil and root bacterial communities. We present a conceptual pipeline for an efficient use of these culture-based and culture-independent platforms to identify novel antimicrobials-producing gene clusters in-vivo.

The second one (a bioRxiv pre-print) utilized some of these techniques to explore differences in secondary metabolites gene clusters between soil and roots bacterial communities, in terms of diversity, composition and taxonomy. We then took advantage of this data and deeply focused on root-enriched and abundant sequences (those that were associated with NRPS and PKS, mega-enzymes that produces two very important families of secondary metabolites- nonribosomal peptides and polyketides). Then, we used a unique culture-independent platform (eSNaPD, from Sean Brady lab @ Rockefeller U, NY) and were able to actually recover 5 clones (~40Kb in length) that harbored five novel gene clusters. At least one of these probably encode for an antifungal metabolites (derived from Actinobacteria). This piepline/platform is applicable for other uses of course, depending on your research question and the functions you’re intrested in. I’ll be happy for any feedback regarding the bioRxiv MS (either directly there or via my tweeter).

General microbiology

Roadmap for naming uncultivated Archaea and Bacteria, Alison E. Murray, Nature Microbiology

Human microbiome

Re-evaluating the relationship between missing heritability and the microbiome, Gavin Douglas , Microbiome

Microbes and mental health: Can the microbiome help explain clinical heterogeneity in psychiatry?, Christina L. Hayes, Front. Neuroendocrinology

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations, Nicolai Karcher, Genome Biology

Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis, Anna Ursula Happel , PLOS Pathogens

Hospital microbiome

Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations, Jessica Chopik , Microbiome

Antibiotic Resistance

The household resistome – frequency of beta-lactamases, class 1 integron and antibiotic resistant bacteria in the domestic environment, Laura S. Schages , bioRxiv

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus, Henrique Machado, bioRxiv

Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis, Yu Pan, mSystems

Bioinformatics

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems, Begum D. Topcuoglu, mBio

PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing, Alexis Robitaille, BMC Bioinformatics

May 12, 2020

Posted on May 12, 2020 by Jose Gracia

Buenos dias!! Greetings from Spain.

Today we can highlight a very interesting article of gut–brain modulation of a monkey model of human depression, MELODY a new trial to improve the future microbiome of the offspring of mothers with Crohn’s disease, or how It’s the fertilization the main agent in rhizosphere composition.

I hope you enjoy reading this as much as I did making it!
Stay safe, Jose

COVID-19

Pre-print: Prediction analysis of SARS-COV-2 entry in Livestock and Wild animals – Manas Ranjan Praharaj et al. – bioRxiv

Pre-print: Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity – Niko Kohmer et al. – bioRxiv

Pre-print: The role of high cholesterol in age related COVID19 lethality. – Hao Wang et al. – bioRxiv

Human vaginal microbiome

Effect of commercial vaginal products on the growth of uropathogenic and commensal vaginal bacteria – Kristin J. Hung et al. – Scientific Reports

Human respiratory microbiome

Differences in airway microbiome and metabolome of single lung transplant recipients – Nirmal S. Sharma et al. – Respiratory Research

Pre-print: Assessing the variation within the oral microbiome of healthy adults – Jacob T. Nearing et al. – bioRxiv

Microbiome profile associated with malignant pleural effusion – Samira Shojaee et al. – PLOS ONE

Composition and function of oral microbiota between gingival squamous cell carcinoma and periodontitis – Yuchao Li et al. – Oral Oncology

Esophageal microbiome signature in patients with Barrett’s esophagus and esophageal adenocarcinoma – Loris Riccardo Lopetuso et al. – PLOS ONE

Human gut microbiome

Subtle Variations in Dietary-Fiber Fine Structure Differentially Influence the Composition and Metabolic Function of GutMicrobiota – Tuncil, Y. E et al. – mSphere

Intestinal parasites in rural communities in Nan Province, Thailand: Changes in bacterial gut microbiota associated with minute intestinal fluke infection – Ajala Prommi et al. – Cambridge University Press

Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease – Michelle R et al. – Journal of the American Society of Nephrology

The gut microbiome modulates gut–brain axis glycerophospholipid metabolism in a region-specific manner in a non-human primate model of depression – Peng Zheng et al. – Molecular Psychiatry

A dietary intervention to improve the microbiome composition of pregnant women with Crohn’s disease and their offspring: The MELODY (Modulating Early Life Microbiome through Dietary Intervention in Pregnancy) trial design – Peter Inga et al. – Contemporary Clinical Trials Communications

Gut Microbiota Dysbiosis Associated with Bile Acid Metabolism in Neonatal Cholestasis Disease – Meng Li et al. – Scientific Reports

Individual and cohort-specific gut microbiota patterns associated with tissue-specific insulin sensitivity in overweight and obese males – Gerben D. A. Hermes et al. – Scientific Reports

Fecal microbiota composition is linked to the postoperative disease course in patients with Crohn’s disease – Anna Strömbeck et al. – BMC Gastroenterology

Human skin microbiome

Diversity of navel microbiome in young adults Free – Shreya Shah et al. – Journal of Medical Microbiology

Animal experiments

Wild primate microbiomes prevent weight gain in germ-free mice – Dimitrios N. Sidiropoulos et al. – Animal Microbiome

Changes in the microbiome of mariculture feed organisms after treatment with a potentially probiotic strain of Phaeobacter inhibens – Karen K. Dittmann et al. – Applied and Environmental Microbiology

Alterations of fecal microbiome characteristics by dietary soy isoflavone ingestion in growing pigs infected with porcine reproductive and respiratory syndrome virus – B N Smith et al. – Journal of Animal Science

Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection – Qiang Zhang et al. – Genome Biology

Pre-print: Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter – Aaron McKenna et al. – bioRxiv

Administration of Bifidobacterium bifidum CGMCC 15068 modulates gut microbiota and metabolome in azoxymethane (AOM)/dextran sulphate sodium (DSS)-induced colitis-associated colon cancer (CAC) in mice – Qing Wang et al. – Applied Microbiology and Biotechnology

Animal microbiome

Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects – My Hanh Le et al. – Scientific Reports

Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus) – Geraint Element et al. – Envariomental microbiology

Honeybee microbiome is stabilized in the presence of propolis – Perot Saelao et al. – Biology letters

Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels – Po-Yu Liu et al. – Scientific Reports

Preprint: Differential Response of Digesta- and Mucosa-Associated Intestinal Microbiota to Dietary Black Soldier Fly (Hermetia illucens) Larvae Meal in Seawater Phase Atlantic Salmon (Salmo salar) – Yanxian Li et al. – bioRxiv

Plant, root, and soil microbiome

Liming reduces N2O emissions from Mediterranean soil after-rewetting and affects the size, structure and transcription of microbial communities – Eduardo Vázquez et al – Soil Biology and Biochemistry

Significant effects on soil microbial communities were not detected after strategic tillage following 44 years of conventional or no-tillage management – Vivian A. Rincon-Florez – Pedobiologia

Seasonal variations in soil microbial communities under different land restoration types in a subtropical mountains region, Southwest China – Denggao Fu et al. – Applied Soil Ecology

Short term effects of biochar with different particle sizes on phosphorous availability and microbial communities – Rubab Sarfraz et al. – Chemosphere

Microbial community responses to different volatile petroleum hydrocarbon class mixtures in an aerobic sandy soil – George Mangse et al.– Environmental Pollution

Plant litter amendments in restored wetland soils altered microbial communities more than clay additions – Christine E. Maietta et al. – Soil Biology and Biochemistry

Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems – Mikhail V. Semenov et al. – Applied Soil Ecology

Effect of compost amendment and bioaugmentation on PAH degradation and microbial community shifting in petroleum-contaminated soil – Manli Wu et al. – Chemosphere

Review: The use of -omics tools for assessing biodeterioration of cultural heritage: A review – GutarowskaBeata – Journal of Cultural Heritage

Water and extremophile

Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells – Sara Gallego et al – Science of The Total Environment

High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater–Sediment Interface of a Deep-Sea Cold Seep in South China Sea – Qing-Lei Sun et al. – Microorganisms

Glacial microbiota are hydrologically connected and temporally variable – Karen A Cameron et al. – Enviromental microbiology

Built environment

The microbiome driving anaerobic digestion and microbial analysis – Jun Wei Lim et al. – Advances in Bioenergy

Bioinformatics

MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data – Nathanael J. Bangayan et al. – Microorganisms

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia – Matthew G Jones et al. – Genome Biology

TaxIt: An iterative computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic single-organism samples – Mathias Kuhring et al. Journal of Proteome Research

Review: The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health – Ameen Eetemadi et al. – Frontiers in Microbiology

General microbiology

Review: Diversity, ecology and evolution of Archaea – Brett J. Baker et al – Nature Microbiology

Microbes on the market

Microbiome Sequencing Services Market 2020-2024 – husain – NJ MMA News

February 28, 2020

Posted on February 28, 2020 by barakdror

Good morning/afternoon y’all! today’s digest features some interesting-to-read genral biotech and ecology papers, as weel as the first gene catalouge of the vaginal microbiome, American pets microbiome revealed, cool microbiome engineering for biocontrol purpose in agriculture, a bunch of salt- and sweet-water microbiome studies and more!

Have a great weekend! put the guilt aside and enjoy some time with your spouse, family, pets, hobbies and anything else that you enjoy!

General Science

is is a very cool paper, beuatifuly presenting the connection and applicatino of two very ‘hot’ topics in today biotechnology world- AI and drug discovery:A Deep Learning Approach to Antibiotic Discovery- A Deep Learning Approach to Antibiotic Discovery, Jonathan M. Stokes, Cell

** Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer, Roman Moscoviz, Trends in Microbiology

A solution to minimum sample size for regressions, David J. Jenkins , PLOS One

The relationship between the host genome, microbiome, and host phenotype, Harald Brussow, Env. Micro.

Human microbiome

** A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina, Bing Ma, Nature Communications

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention, Jessica A. Grembi, Sci. Rep.

Analysis of healthy reference ranges for clinically relevant gut microbial indicators: A large web-based cohort study in Japan, Satoshi Watanabe , bioRxiv

Short chain fatty acids produced by colonizing intestinal commensal bacterial interaction with expressed breast milk are anti-inflammatory in human immature enterocytes, Nan Zheng, PLOS One

Animal microbiome

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach, Aashish R. Jha, PLOS One

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome, Samuel J. Bowers, PLOS One

Insect microbiome

**Engineering bacterial symbionts of nematodes improves biocontrol potential of the western corn rootworm, Ricardo A. R. Machado, Nature Biotechnology

Plant and soil microbiome

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome, Siwen Deng , bioRxiv

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes, Yuting Liang , Env. Micro.

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria, Qiolong Hu , npj biofims and microbiomes

Marine microbiome

Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings, Marcela Franca Dias, Water Research

Niche partitioning of methane-oxidizing bacteria along the oxygen–methane counter gradient of stratified lakes, Magdalena J. Mayr, ISME

A metagenomic assessment of microbial eukaryotic diversity in the global ocean, Aleix Obiol, Mol. Eco. Res.

Ocean acidification affects microbial community and invertebrate settlement on biofilms, Katie S. Nelson, Sci. Rep.

Understanding and creating biocementing beachrocks via biostimulation of indigenous microbial communities, Asha A. Ramachandran , Env. Biotech.

October 11, 2019

Posted on October 11, 2019 by barakdror

Good morning everyone!

Today’s digest is full of great reviews paper, among else- from the gut microbiome to bacterial metabolic modelling. Also featured is a lovely paper regarding vaginal microbiome transplantation (with interesting translational meaning!) and a food-for-thought paper about microbiology past, present and furture (1st in the list down).

Have a great weekend and happy Jewish New year!

Food for Thought

Shift in the paradigm towards next-generation microbiology, Blaz Sterz & Luka Kronegger, FEMS Microbiology Letters

Human microbiome

** Re‐assessing microbiomes in the low‐biomass reproductive niche, Jessica L. O’Callaghan, BJOG

** Incorporating functional trade-offs into studies of the gut microbiota, Aspen T Reese, Curr. Opi. Microbiology

** Gut microbial metabolites in depression: understanding the biochemical mechanisms, Giorigia Caspani, microbial cell

** Vaginal microbiome transplantation in women with intractable bacterial vaginosis, Ahinoam Lev-Sagie, Nature Medicine

Gut microbiome diversity is associated with sleep physiology in humans, Robert P. Smith, PLOS One

Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties, P.I. Diaz, J. Dental Research

Animal microbiome

A wild microbiome improves mouse modeling of the human immune response, Sara E. Hamiltion, Lab Animal

Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability, Duy Le, Microbial Ecology

Environmental microbiome

** Implications of indoor microbial ecology and evolution on antibiotic resistance, Sarah Ben Maamar, J. Exp. science & Env. Epid.

A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability, O. Nicolitch, Scientific Reports

Preceding crop and tillage system affect winter survival of wheat and the fungal communities on young wheat roots and in soil, Hanna Friberg, FEMS Microbiology Letters

Viral microbiome

A review on viral metagenomics in extreme environments, Sonia Davila-Ramos, Frontiers in Microbiology

Methods in microbiology

Multi-faceted approaches to discovering and predicting microbial nutritional interactions, Sebastian Gude, Curr. Opi. Biotechnology

Artificial neural network-assisted Fourier transform infrared spectroscopy for differentiation of Salmonella serogroups and its application on epidemiological tracing of Salmonella Bovismorbificans outbreak isolates from fresh sprouts, Helene Obereuter, FEMS Microbioogy Letters

August 15, 2018

Posted on August 15, 2018 by edwardmessick

A nice crop of plant/root/soil microbiome studies, some interesting analyses of early life/pregnancy and vaginal microbiota, a belly-load of gut microbiome science, a herd of animal studies, and a few really bad puns… Enjoy!

Events and jobs

A summary of the third annual HIV microbiome workshop – Dr. Brett Williams – AIDS Research and Human Retroviruses

Pregnancy and early life

Early childhood antibiotics use and autism spectrum disorders: a population-based cohort study – Amani F Hamad – International Journal of Epidemiology

The effects of gut microbiota on metabolic outcomes in pregnant women and their offspring – You Lv – Food & Function

Human vaginal microbiome

Cervicovaginal microbiota, women’s health, and reproductive outcomes – Samuel J. Kroon – Fertility and Sterility

Relevance of assessing the uterine microbiota in infertility – Inmaculada Moreno – Fertility and Sterility

Cervicovaginal microbiota, women’s health, and reproductive outcomes – Samuel J. Kroon – Fertility and Sterility

Human nearly-sterile sites

Ursodeoxycholic acid improves liver function via phenylalanine/tyrosine pathway and microbiome remodelling in patients with liver dysfunction – Da Jung Kim – Scientific Reports

Human gut microbiome

Assessing antibiotic resistance gene load in vegan, vegetarian and omnivore human gut microbiota – Losasso Carmen – International Journal of Antimicrobial Agents

Immunomodulatory tetracyclines ameliorate DNBS-colitis: Impact on microRNA expression and microbiota composition – J. Garrido-Mesa – Biochemical Pharmacology

Effects of anthocyanins from the fruit of Lycium ruthenicum Murray on intestinal microbiota – Yamei Yan – Journal of Functional Foods

Disparate Effects of Antibiotics on Hypertension – Sarah Galla – Physiological Genomics

Variability of core microbiota in newly diagnosed treatment-naïve paediatric inflammatory bowel disease patients – T. G. J. de Meij – PLOS One

Dietary soybean protein ameliorates high-fat diet-induced obesity by modifying the gut microbiota-dependent biotransformation of bile acids – Keita Watanabe – PLOS One

* Gut microbiota alterations in moderate to severe acne vulgaris patients – Hui‐Min Yan – The Journal of Dermatology

Implication of gut microbiota metabolites in cardiovascular and metabolic diseases – Francois Brial – Cellular and Molecular Life Sciences

Making Sense of… the Microbiome in Psychiatry – Thomaz F S Bastiaanssen – International Journal of Neuropsychopharmacology

The Microbiome in Cirrhosis and its Complications – Chathur Acharya – Clinical Gastroenterology and Hepatology

Lactobacillus rhamnosus GG induced protective effect on allergic airway inflammation is associated with gut microbiota – Juan Zhang – Cellular Immunology

The gut microbiome as a driver of individual variation in cognition and functional behaviour – Gabrielle L. Davidson – Philosophical Transactions of the Royal Society B

Animal experiments

The impact of Clostridium butyricum MIYAIRI 588 on the murine gut microbiome and colonic tissue – Mao Hagihara – Anaerobe

Monitoring and evaluation of the interaction between deoxynivalenol and gut microbiota in Wistar rats by mass spectrometry-based metabolomics and next-generation sequencing – Eugènia Miró-Abella – Food and Chemical Toxicology

Lentil (Lens culinaris Medikus) Diet Affects the Gut Microbiome and Obesity Markers in Rat – Niroshan Siva – Journal of Agricultural and Food Chemistry

Gut bacterial composition in a mouse model of Parkinson’s disease – P. Perez-Pardo – Beneficial Microbes

Gut Microbiome in BALB/c and C57BL/6J Mice Undergoing Experimental Thyroid Autoimmunity Associate with Differences in Immunological Responses and Thyroid Function – Sajad Moshkelgosha – Hormone and Metabolic Research

Ultraviolet Irradiation of Skin Alters the Faecal Microbiome Independently of Vitamin D in Mice – Simon Ghaly – Nutrients

Impact of lincosamides antibiotics on the composition of the rat gut microbiota and the metabolite profile of plasma and feces – C. Behr – Toxicology Letters

Animal microbiome

Understanding bacterial communities for informed biosecurity and improved larval survival in Pacific oysters – Olivier Laroche – Aquaculture

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota – Fernanda Cornejo-Granados – PeerJ

Do the microorganisms from laboratory culture spent growth medium affect house dust mite fitness and microbiome composition? – Vit Molva – Insect Science

Plant, root, and soil microbiome

Microbial diversity associated to the intestinal tract of soil invertebrates – Dayana da Silva Correia – Applied Soil Ecology

Yellow Canopy Syndrome in sugarcane is associated with shifts in the rhizosphere soil metagenome but not with overall soil microbial function – Kelly Hamonts – Soil Biology and Biochemistry

Anthropogenic influence shapes the distribution of antibiotic resistant bacteria (ARB) in the sediment of Sundarban estuary in India – Anish Bhattacharyya – Science of the Total Environment

Disentangling effects of temperature on microbial community and copper extraction in column bioleaching of low grade copper sulfide – Yuguang Wang – Bioresource Technology

Long-term Plastic Greenhouse Cultivation Changes Soil Microbial Community Structures: A Case Study – Yang Song – Journal of Agricultural and Food Chemistry

Flooding and prolonged drought have differential legacy impacts on soil nitrogen cycling, microbial communities and plant productivity – Linh T. T. Nguyen – Plant and Soil

[PhD Dissertation] Microbial Communities and Their Impact on Bioenergy Crops in Dynamic Environments – Brandon Monier, South Dakota State University – Open Prairie

[PDF] Characterization of osmotolerant rhizobacteria for plant growth promoting
activities in vitro and during plant-microbe association under osmotic stress – Bandeppa – Indian Journal of Experimental Biology

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments – Morgan R. McPherson – J. Vis. Exp

Water and extremophile microbiome

[PDF download] Monitoring biofilm communities in operational drinking water distribution systems and the impact on water quality – I. Douterelo – 1st International WDSA

Molecular detection of microbial communities associated with Microcystis vs Synechococcus dominated waters in Tianjin, China – Da Huo – Journal of Oceanology and Limnology

Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia – Katherine Bedoya – Science of the Total Environment

Profiling microbial communities in a watershed undergoing intensive anthropogenic activities – Hehuan Liao – Science of the Total Environment

The gut microbiome and aquatic toxicology: An emerging concept for environmental health – Ondrej Adamovsky – PeerJ

Microbial community composition of a hydrocarbon reservoir 40 years after a CO2 enhanced oil recovery flood – Jenna L K Shelton – FEMS Microbiology Ecology

Temporal dynamics of activated sludge bacterial communities in two diversity variant full-scale sewage treatment plants – Xiao-Tao Jiang – Applied Microbiology and Biotechnology

The Nile River Microbiome Reveals a Remarkably Stable Community Between Wet and Dry Seasons, and Sampling Sites, in a Large Urban Metropolis (Cairo, Egypt) – Eraqi WA – OMICS

Probiotics / prebiotics

Influence of monostrain and multistrain probiotics on immunity, intestinal ultrastructure and microbiota in experimental dysbiosis – E. Ermolenko – Beneficial Microbes

Effects of Probiotics on Inflammation and Uremic Toxins Among Patients on Dialysis: A Systematic Review and Meta-Analysis – Charat Thongprayoon – Digestive Diseases and Sciences

Bioinformatics

Biomarker panels for characterizing microbial community biofilm formation as composite molecular process – Magnus Bosse – PLOS One

* Maximal viral information recovery from sequence data using VirMAP – Nadim J Ajami – Nature Communications

Techniques

Using Bioreactors to Study the Effects of Drugs on the Human Microbiota – Mabel Guzman-Rodriguez – Methods

Ed’s non-microbiology picks

Human activities might influence oncogenic processes in wild animal populations – Mathieu Giraudeau – Nature Ecology & Evolution

In apoptosis, cell death spreads through perpetuating waves – James Ferrell – Stanford Medicine

Study finds Tdap vaccination for pregnant women does not increase risk of autism

Boys should be given HPV vaccine, says joint committee

New Study: Omega-3s Can Help Keep Kids Out of Trouble

Mars (probably) has a lake of liquid water

June 22, 2018

Posted on June 22, 2018 by ashokksharma08

Have a happy weekend! Today in Microbiome Digest: reviews on microbiome immunity and type 1 diabetes, metatranscriptome analysis of vaginal microbiome, Differences in gut microbiota associated with age, sex, and stool consistency, microbes in the news, and more…

Events and jobs

Scientist – Genomics and Microbiome – Madison, WI

Bioinformatics Scientific Programmer – Quadram Institute Bioscience

General microbiome

Review: Communication Between the Microbiota and Mammalian Immunity – Kyla S. Ost – Annual Review of Microbiology

Host genotype-specific microbiota do not influence the susceptibility of D. magna to a bacterial pathogen – Marilou P. Sison-Mangus – Scientific Reports

Pregnancy and early life

Book chapter: Implantation Failure 1: Intrauterine Circumstances and Embryo–Endometrium Synchrony at Implantation – Keiji Kuroda – Treatment Strategy for Unexplained Infertility and Recurrent Miscarriage

Special Issue: Microbiome in normal and pathological pregnancies: A literature overview – Carla R. Taddei – American Journal of Reproductive Immunology

Multi-site human microbiome

Bacterial invasion of dentinal tubules from the external root surface with and without an intact cemental layer- a confocal laser scanning microscopic study – Jovita D’souza – Advances in Tissue Engineering and Regenerative Medicine

Human respiratory microbiome