Category Archives: Uncategorized

May 16th, 2020

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Good morning!

A few nice studies today, with highlights being utilising Streptomyces endophytes to aid in plant growth, a review on the gut-brain-axis with a focus on psychiatry, and a bioinformatics study looking into the role of pathogenic E.coli in cancer. Enjoy!

COVID-19

The coding capacity of SARS-CoV-2 Y.Finkel/O. Mizrahi et al. bioXriv.

Human vaginal microbiome

The study of host-bacterial relationships and immune function in different vaginal environments (Study in progress) A. berard et al. Journal of Obstetrics and Gynaecology Canada.

Human gut microbiome

Relationship between the composition of the digestive microbiota and the concentrations of opportunistic pathogens in intensive care patients. C. Fontaine et al. bioXriv.

Animal microbiome

Evaluation of fecal Lactobacillus populations in dogs with idiopathic epilepsy: a pilot study. Karen R. Muñana et al. Animal microbiome.

Plant, root and soil microbiome

Streptomyces endophytes promotes the growth of Arabidopsis thaliana S. F Worsley et al. bioXriv.

Water and extremophile microbiome

Deciphering a marine bone degrading microbiome reveals a complex community effort E. Borchert et al. bioRxiv.

Prebiotics

Human microbiome and homeostasis: insights into the key role of prebiotics, probiotics and symbiotics. B. Salehi et al. Critical Reviews in Food Science and Nutrition.

Probiotics and the Microbiota-Gut-Brain Axis: Focus on Psychiatry. Mörkl S. Current Nutrition Reports.

Bioinformatics

Novel Discoveries Targeting Pathogenic Gut Microbes and New Therapies in Pancreatic Cancer: Does Pathogenic E. coli Infection Cause Pancreatic Cancer Progression Modulated by TUBB/Rho/ROCK Signaling Pathway? A Bioinformatic Analysis. W. Luo et al. BioMed Research international.

May 15th, 2020

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We have got a balanced mix for folks today of human, animal, plant, and free-living microbiome research. In particular I want to highlight the work of Inagaki et al., who tracked gut microbiome dynamics within Japanese termites (Reticulitermes speratus) during dispersal and colony formation. They observed a rapid increase then decrease of gut protozoa coinciding with larval hatching of a pioneering termite pair’s first brood; a pattern they call a ‘gut microbial pulse’ (what a wonderfully evocative term!). This is a neat example of how host-associated microbiomes might play a integral role in the ecology of free-living organisms.

General microbiome

Dynamic metabolic adaptation can promote species coexistence in competitive communities– Leonardo Pacciani-Mori et al. – PLOS Computational Biology

The role of the microbiota in periodontal disease – Mike A. Curtis et al. – Periodontology 2000

Human respiratory microbiome

Oral‐lung microbiome interactions in lung diseases– Manoj J. Mammen et al. – Periodontology 2000

Human nearly-sterile sites

Microbiome and Schizophrenia: Current Evidence and Future Challenges – Thiago Macedo e Cordeiro et al. – Current Behavioural Neuroscience Reports

Human gut microbiome

Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota – Sivaranjani Namasivayam et al. – PLOS Neglected Tropical Diseases

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type – Alan Le Goallec et al. – PLOS Computational Biology

The role of small intestinal bacterial overgrowth and false positive diagnosis of lactose intolerance in southwest Hungary — A retrospective observational study – Péter Varjú et al. – PLOS One

The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile – Monique J.T Crobach et al. – Microorganisms

Animal experiments

Effect of age and the individual on the gastrointestinal bacteriome of ponies fed a high-starch diet– Philippa K. Morrison et al. – PLOS One

Animal microbiome

Gut microbial pulse provides nutrition for parental provisioning in incipient termite colonies – Tatsuya Inagaki et al. – Behavioural Ecology and Sociology

The role of the gut microbiome in mediating standard metabolic rate after dietary shifts in the viviparous cockroach, Diploptera punctata – Paul A. Ayayee et al. – Journal of Experimental Biology

Plant, root, and soil microbiome

Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering – Joël Klein et al. – PlOS One

Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis – Maria Kazou et al. – Microorganisms

Quantifying Plant-Borne Carbon Assimilation by Root-Associating Bacteria – Spenser Waller et al. – Microorganisms

Water and extremophile microbiome

Community-level signatures of ecological succession in natural bacterial communities – Alberto Pascual-Garcia & Thomas Bell – Nature Communications

Instigation of indigenous thermophilic bacterial consortia for enhanced oil recovery from high temperature oil reservoirs – Leha Sharma et al. – PLOS One

Microplastics affect sedimentary microbial communities and nitrogen cycling – Meredith E. Seeley et al. – Nature Communications

Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient – James Seward et al. – Environmental Microbiology

Techniques

Confocal Raman microscopy to identify bacteria in oral subgingival biofilm models – Lukas Simon Kriem et al. – PLOS One

 

Probiotics to precision probiotics

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After “precision medicine”, it is now time to conceptualize the term “precision probiotics”. In simple words, fundamental idea of precision medicine is to develop “new taxonomy” of disease employing molecular characterization of disease based on individual data that will enable better stratification of patients and determining most effective treatments. On similar lines, Veiga and colleagues offer strategies to develop precision probiotics, combine with multi-omics host response data to find most optimal probiotic modality in stratified individuals/populations.

I would recommend to read the review in full. To motivate you, following are some excerpts from the review:

“Historically, the discovery of probiotics relied on a top-down approach, where a microorganism enriched in healthy individuals (compared to an altered health state) is suggested to be beneficial and correlates with a health benefit upon administration to humans…While this empirical top-down approach provides robust leads for the development of probiotics, in the absence of prior mechanistic information, it inherently necessitates multiple cycles of trial and error to identify health benefits.”

Problems with top-down approach

  • “Probiotic efficacy being both strain- and indication-specific
  • Person-specific factors also contribute to heterogeneity in the outcome of probiotic supplementations, including diet, age and the microbiome. Colonization-resistant microbiomes are more resilient to probiotic interventions compared to colonization-permissive individuals.”

Bottom up approach

“The phenotypic approach is based on screening for probiotic effects using in vitro and ex vivo cell cultures as well as animal models with immune, neuronal, metabolic or microbial read-outs.

Target-based discovery relies on the selection of probiotic candidates based primarily on in silico prediction of their capacity to produce molecular effectors that are potentially able to modulate host or microbial pathways, which are foreseen to play a critical role in health or disease. Such in silico predictions would require the use of multi-omics (such as genomics, transcriptomics, metabolomics and proteomics) possibly coupled to metabolic reconstruction to infer the metabolic capacity of the screened microorganisms.”

Challenges with bottom-up approach

  • “A greater challenge lies in applying a person-specific approach to predict efficacy, which likely requires obtaining profound individualized host data (including genetics, anthropometrics and immune profiling) and microbiome data (such as strain-level composition, transcriptomics and metabolomics), as well as identifying relevant biomarkers that predict colonization resistance and/or a health outcome.
  • As stool samples do not accurately reflect colonization and impact on the gut microbiota along the gastrointestinal tract during probiotic supplementation, there is a great need to devise non-invasive means for identifying compatible probiotic–individual matches.
  • Another important factor to consider is safety, as exogenous microorganisms can have unexpected effects on the microbiome, and can even compromise the health of vulnerable subjects and result in bacteraemia or fungaemia.”

I believe that these challenges also hold true for top-down approach

Precision probiotics strategies

The big aim

“…developing algorithms that, when provided with these individualized parameters, can suggest the optimal probiotic modality that would result in a beneficial outcome.”

  • “To achieve this goal, on one hand, scientists need to better characterize the physiological or pathological pathways that can be modulated by probiotics, in line with the increasing effort to use bottom-up approaches.
  • On the other hand, further digitization of tools for the collection and processing of person-specific data, and their integration with genomic and metabolomic host and microbiome profiles, will be required.
  • Setting up standardized protocols that allow bio-citizens to self-experiment in ‘N-of-1 trials’ and report their experiences with probiotics, coupled with individualized measurements, would greatly expand our understanding of differential probiotic activity in the heterogenous human population. This approach will require devising strict validation and safety measurements for promising centralized data collection while maintaining participants’ anonymity.“

“…While today, this (refers to microbiome data) personal information is poorly actionable, tomorrow it could serve as the basis for microbiome-centred precision nutrition and preventive medicine, including precision probiotics.”

May 13, 2020

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Happy Wednesday, y’all! Before we get to today’s papers, I wanted to let everyone know about a webinar happening on June 3rd at 12:00 PM E.T. called “Unraveling the link between the gut microbiome, human health, and disease.” Tomoya Yamashita, M.D., Ph.D. from Kobe University Graduate School of Medicine and Meredith Hullar, Ph.D. from the Fred Hutchinson Cancer Research Center will both be speaking. If you’re interested you can register here.

Now onto the highlights! We have some super interesting research to share with you today including an examination of the efficacy of transplanting the human gut microbiota into mice and its impact on studying immunological responses; evidence that early-life intestinal colonizers may influence brain development; and a new tool, pepFUNK, which uses a peptide-centric approach to identify KEGG pathways in metaproteomic datasets. Enjoy!

General microbiome
Human Microbiota-Transplanted C57BL/6 Mice and Offspring Display Reduced Establishment of Key Bacteria and Reduced Immune Stimulation Compared to Mouse Microbiota-Transplantation. Lundberg, R. et al. Scientific Reports.

Review: The role of the microbiome in the neurobiology of social behaviour. Sarkar, A. et al. Biological Reviews.

Pregnancy and early life
Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula. Brink, L.R. et al. The American Journal of Clinical Nutrition.

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers. Lugli, A.G. et al. FEMS Microbiology Ecology.

Human respiratory microbiome
Bioorthogonal Non-Canonical Amino Acid Tagging Reveals Translationally Active Subpopulations of the Cystic Fibrosis Lung Microbiota. Valentini, T.D. et al. Nature Communications.

Human gut microbiome
Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 With Clostridia and Insulin Sensitivity in Humans. Zhou, X. et al. Diabetes.

Berberine and Its Structural Analogs Have Differing Effects on Functional Profiles of Individual Gut Microbiomes. Li, L. et al. Gut Microbes.

Animal experiments
Developmental Signatures of Microbiota-Derived Metabolites in the Mouse Brain. Swann, J.R. et al. Metabolites.

Bifidobacteria Shape Host Neural Circuits During Postnatal Development by Promoting Synapse Formation and Microglial Function. Luck, B. et al. Scientific Reports.

Glycerol Monolaurate, an Analogue to a Factor Secreted by Lactobacillus, Is Virucidal Against Enveloped Viruses, Including HIV-1. Welch, J.L. et al. mBio.

Gut Microbiome Communication With Bone Marrow Regulates Susceptibility to Amebiasis. Burgess, S.L. et al. The Journal of Clinical Investigation.

The Protective Effects of 2′-Fucosyllactose Against E. Coli O157 Infection Are Mediated by the Regulation of Gut Microbiota and the Inhibition of Pathogen Adhesion. Wang Y. et al. Nutrients.

Capsaicin Improves Glucose Homeostasis by Enhancing Glucagon-Like peptide-1 Secretion Through the Regulation of Bile Acid Metabolism via the Remodeling of the Gut Microbiota in Male Mice. Hui, S. et al. FASEB Journal.

Microbiota-Induced Type I Interferons Instruct a Poised Basal State of Dendritic Cells. Schaupp L. et al. Cell.

Intratumoral Accumulation of Gut Microbiota Facilitates CD47-based Immunotherapy via STING Signaling. Shi, Y. et al. Journal of Experimental Medicine.

Animal microbiome
Housefly (Musca domestica L.) associated microbiota across different life stages. de Jonge, N. et al. Scientific Reports.

Honey-bee–associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. Deboutte, W. et al. PNAS.

Bayesian Modeling Reveals Host Genetics Associated With Rumen Microbiota Jointly Influence Methane Emission in Dairy Cows. Zhang, Q. et al. ISME Journal.

Review: The role of the gut microbiome in sustainable teleost aquaculture. Perry, W.B. et al. Proceedings of the Royal Society B.

Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Wikberg E.C. Animal Behaviour.

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. et al. FEMS Microbiology Ecology.

Probiotics / prebiotics
A Human-Origin Probiotic Cocktail Ameliorates Aging-Related Leaky Gut and Inflammation via Modulating the Microbiota/Taurine/Tight Junction Axis. Ahmadi, S. et al. JCI Insight.

Bioinformatics
SHOGUN: A Modular, Accurate, and Scalable Framework for Microbiome Quantification. Hillmann, B. et al. Bioinformatics.

pepFunk: A Tool for Peptide-Centric Functional Analysis of Metaproteomic Human Gut Microbiome Studies. Simopoulos, C.M.A. et al. Bioinformatics.

Microbes in the news
Mapping the Microbiome in Saliva of COVID-19 Patients.

Inside the Belly of the Horse – Doctoral candidate Alexa Johnson goes inside the gut to investigate equine health.

May 12, 2020

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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

May 9, 2020

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Among the highlights for today, there’s an unusual preprint on using honeybees for proxy sampling of the urban microbiome, as well as a paper on the effect of captivity on the microbiome of raptors.

In some non-microbiome related news, the summarized highlights from the 5th International One Health Congress were recently published. Some of their recommendations regarding science and public health are particularly apt considering the present pandemic, and I found it to be quite an interesting read. You can find it here:

Make science evolve into a One Health approach to improve health and security: a white paper – Osterhaus et al. – One Health Outlook

I hope you’re all doing well, wherever you are!

COVID-19

Preprint: The coding capacity of SARS-CoV-2 – Finkel et al. – bioRxiv

Pregnancy and early life

An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community – Koo et al. – Royal Society of Open Science

Animal microbiome

Preprint: Host evolutionary history and ecology shape virome composition in fishes – Geoghegan et al. – bioRxiv

The fecal microbiota of wild and captive raptors – Oliveira et al. – Animal Microbiome

Plant, root, and soil microbiome

Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? – Kaplan et al. – Evolutionary Applications

Built environment

Preprint: Holobiont urbanism: sampling urban beehives reveals cities’ metagenomes – Henaff et al. – bioRxiv

Techniques

Preprint: Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution – Matsuo et al. – bioRxiv

Quantifying technical confounders in microbiome studies – Bartolomaeus et al. – Cardiovascular Research

May 3, 2020

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COVID19
Preprint: Lack of Reinfection in Rhesus Macaques Infected with SARS-CoV-2 – Bao – Biorxiv

Events and jobs

Call for papers: BMC Health Policy and the Management of Antimicrobial Resistance in LMICs

Pregnancy and early life

Hospital Regimens Including Probiotics Guide the Individual Development of the Gut Microbiome of Very Low Birth Weight Infants in the First Two Weeks of Life – Kurath-Koller – Nutrients

Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery – Hernandez – Scientific Reports


Human gut microbiome

Review: The link between autism spectrum disorder and gut microbiota: A scoping review – Nitschke – Autism


Intestinal Dysbiosis in Carriers of Carbapenem-Resistant Enterobacteriaceae – Korach-Rechtman – mSphere

Human oral microbiome
Review: Oral microbiome: possible harbinger for children’s health – Xiao – International Journal of Oral Science

Animal experiments

Komagataeibacter hansenii CGMCC 3917 Alleviates Alcohol-Induced Liver Injury by Regulating Fatty Acid Metabolism and Intestinal Microbiota Diversity in Mice – Lin – Royal Society of Chemistry


Putting the microbiota to work: Epigenetic effects of early life antibiotic treatment are associated with immune-related pathways and reduced epithelial necrosis following Salmonella Typhimurium challenge in vitro – Costa – PlosOne


Combined Prebiotic and Microbial Intervention Improves Oral Cholera Vaccination Responses in a Mouse Model of Childhood Undernutrition – Di Luccia – Cell Host & Microbe

Animal microbiome

Establishment and Stability of the Murine Oral Microbiome – Abusleme – Journal of Dental Research

Effect of stocking density and effective fiber on the ruminal bacterial communities in lactating Holstein cows – Clemmons – PeerJ

Plant, root, and soil microbiome

Long-term continuously monocropped peanut significantly changed the abundance and composition of soil bacterial communities – Chen – PeerJ


Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes – Lori – Scientific Reports


Organic mulching positively regulates the soil microbial communities and ecosystem functions in tea plantation – Zhang – BMC Microbiology

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov. – Wang – Microbiology Society


Bioprospecting and characterization of pigmented halophilic archaeal strains from Algerian hypersaline environments with analysis of carotenoids produced by Halorubrum sp. BS2 – Sahli – Journal of Basic Microbiology


Effects of a deep-sea mining experiment on seafloor microbial communities and functions after 26 years – Vonnahme – Science Advances

Food microbiology

Review: Traditionally fermented pickles: How the microbial diversity associated with their nutritional and health benefits? – Behera – Journal of Functional Foods

Bioinformatics

Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control – Bichat – Frontiers in Microbiology


Techniques
Preprint: Freshwater monitoring by nanopore sequencing – Urban – Biorxiv

May 2nd, 2020

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Another month has passed! Hope everyone is staying at home and being well. Today’s highlights include a paper applying NMR to monitor neonatal metabolic adaptations, how oil influence microbial community assembly off the Gulf of Mexico and a preprint for a Bayesian Multi-task method to identify global microbiome associations.

COVID-19 Articles 

Why the Coronavirus Is So Confusing – Ed Yong – The Atlantic

Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals – Liu & Ning et al. – Nature

Human microbiome

Fucosidases from the human gut symbiont Ruminococcus gnavus – Wu & Rebello et al. – Cellular and Molecular Life Sciences

Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection – Grier et al. – bioRxiv **preprint**

Sex-specific Alterations in the Urinary and Tissue Microbiome in Therapy-naïve Urothelial Bladder Cancer Patients – Pederzoli et al.  – European Urology Oncology

Microbiome and Metabolomics 

Metabolic changes in early neonatal life: NMR analysis of the neonatal metabolic profile to monitor postnatal metabolic adaptations – Georgakopoulou, I., Chasapi, S.A., Bariamis, S.E. et al – Metabolomics

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics – Vrieling & Kostidis et al. – Nature Scientific Reports

Soil microbiome

Structural and microbial evidence for different soil carbon sequestration after four-year successive biochar application in two different paddy soils – Bi & Cai et al. – Chemosphere

Soil pH and C/N ratio determines spatial variations in soil microbial communities and enzymatic activities of the agricultural ecosystems in Northeast China: Jilin Province case – Xu et al. – Applied Soil Ecology

Animal microbiome

Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer – Liu & Wang et al. – Virology Journal

Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen & Cormican et al. – PLOS One

Microbiomes of the built environment 

Influence of oil, dispersant, and pressure on microbial communities from the Gulf of Mexico – Noirungsee et al. – Nature Scientific Reports

Passenger-surface microbiome interactions in the subway of Mexico City – Vargas-Robles et al.  – bioRxiv **preprint**

Pathogens 

Intra-species signaling between Pseudomonas aeruginosa genotypes increases production of quorum sensing controlled virulence factors – Mould et al. – bioRxiv **preprint**

Statistics and bioinformatics 

A Bayesian Multi-Task Approach for Detecting Global Microbiome Associations – Hatami et al. – bioRxiv (soon to be published in Bioinformatics) **preprint**

Extremophiles

Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant a-amylase – Deutch & Yang – Antonie van Leeuwenhoek

Aquatic environments  

Cyanobacteria in inland waters: new monitoring, reporting, modelling and ecological research – Mitrovic et al. – Marine & Freshwater Research **review**

Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China – Tang et al. – Environmental Microbiome

Microbiome in the News

Coffee plants have a small but consistent core microbiome of fungi and bacteria – American Phytopathological Society – EurekAlert!

April 30, 2020

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Hello everyone! I hope you are all staying safe and healthy.

COVID-19/SARS-CoV-2

[Preprint]: Evaluation of 19 antiviral drugs against SARS-CoV-2 Infection – Liu et al.

Multi-site human microbiome

[Preprint] Topologically correct synthetic reconstruction of pathogen social behavior found in deep tissue sites – Clark et al.

Human gut microbiome

Association of Short-Chain Fatty Acids in the Gut Microbiome With Clinical Response to Treatment With Nivolumab or Pembrolizumab in Patients With Solid Cancer Tumors – Nomura et al. – JAMA Network

Genetic and metabolic links between the murine microbiome and memory – Mao et al. – BMC

Drosophila as a model for the gut microbiome – Ludington & Ja – PLOS Pathogens

Human respiratory microbiome

Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter? – Angebault et al. – PLOS One

Human oral microbiome

Oral Microbiome Profiling in Smokers with and without Head and Neck Cancer Reveals Variations Between Health and Disease – Sharma et al. – Cancer Prevention Research

Animal microbiome

Coculturing of Mosquito‐Microbiome Bacteria Promotes Heme Degradation in Elizabethkingia anophelis – Ganely et al. – Chemistry Europe

Plant and soil microbiome

The responses of the soil bacterial communities and enzyme activities to the edaphic properties of coal mining areas in Central China – Sun et al. – PLOS One

Water and extremophile microbiome

Network-directed efficient isolation of previously uncultivated Chloroflexi and related bacteria in hot spring microbial mats – Xian et al – Nature

Microbes in space

Crewmember microbiome may influence microbial composition of ISS habitable surfaces – Avila-Herrera et al. – PLOS One

Phages

Structure and conformational cycle of a bacteriophage-encoded chaperonin – Bracher et al. – PLOS One

Technology

An open-source robotic platform that enables automated monitoring of replicated biofilm cultivations using optical coherence tomography – Gierl et al. – Nature

April 29, 2020

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Hello Everyone. Today the Microbiome Digest brings you the latest on Plant-microbial interaction together with a variety of your usual microbiome related research publications. Enjoy.

COVID-19:

Neuraxial anaesthesia and peripheral nerve blocks during the COVID-19 pandemic: a literature review and practice recommendations. – Uppal V. et al. – Anaesthesia.

General microbiome:

The link between autism spectrum disorder and gut microbiota: A scoping review – Nitschke A. et al. – Autism.

General microbiome:

Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter? – Angebault C. et al. – PloS One.

Randomised clinical trial: faecal microbiota transplantation versus autologous placebo administered via colonoscopy in irritable bowel syndrome. – Lahtinen et al. – Aliment Pharmacol Ther.

High L-carnitine ingestion impairs liver function by disordering gut bacteria composition in mice. – Wu Q. et al. – J Agric Food Chem.

Plant, root, and soil microbiome:

Microbiome-Mediated Stress Resistance in Plants – Liu H et al. – Trends in Plant Science.

A plant genetic network for preventing dysbiosis in the phyllosphere – Chen T et al. – Nature.

Harnessing rhizosphere microbiomes for drought-resilient crop production – de Vries et al. – Science

Plant nutrient‐acquisition strategies drive topsoil microbiome structure and function – Bahram et al. – New Phytologist.

Impacts of directed evolution and soil management legacy on the maize rhizobiome – Schmidt JE et al. – Soil Biology and Biochemistry.

Environmental microbiome:

Metal-induced bacterial interactions promote diversity in river-sediment microbiomes. – Cyriaque V. et al. – FEMW Microbiol Ecol.