July 7, 2020

Today’s digest features the mighty sourdough microbiome, AGNOSTOS (a computational workflow for genes annotation using clustering and remote homology detection, contextualizing them with genomic and environmental information), and a new episode of the Bioinformatics Chat podcast about reproducible pipelines and NGLess (a user-friendly domain-specific programming language for NGS data processing), and more. Happy reading/listening!

General microbiome

Microbiome definition re-visited: old concepts and new challenges – Gabriele Berg – Microbiome

Positive interactions are common among culturable bacteria – Jared Kehe – bioRxiv

Gut microbiome

An emerging role of Prevotella histicola on estrogen-deficiency induced bone loss through the gut microbiota-bone axis – Zhongxiang Wang – bioRxiv

Identifying novel high-impact rare disease-causing mutations, genes and pathways in exomes of Ashkenazi Jewish inflammatory bowel disease patients – Yiming Wu – medRxiv

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting – Yang Liu – medRxiv

GWAS of stool frequency reveals genes, pathways, and cell types relevant to human gastrointestinal motility and irritable bowel syndrome – Ferdinando Bonfiglio – medRxiv

Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson’s disease – Velma Aho – medRxiv

Lung microbiome

Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung – Adrian Kordes – Nature Communications

Genitourinary microbiome

Architecture and function of human uromodulin filaments in urinary tract infections – Gregor L. Weiss – Science

The structure and diversity of strain level variation in vaginal bacteria – Brett A. Tortelli – bioRxiv

Synchronous genitourinary lichen sclerosus signals a distinct urinary microbiome profile in men with urethral stricture disease – Andrew J. Cohen – World Journal of Urology

Human urine 1H NMR metabolomics reveals alterations of the protein and carbohydrate metabolism when comparing habitual Average Danish diet vs. healthy New Nordic diet – Alessia Trimigno – Nutrition

Animal experiments

Lactobacillus rhamnosus probiotic prevents airway function deterioration and promotes gut microbiome resilience in a murine asthma model – Irina Spacova – Gut Microbes

Food microbiome

*The Sourdough Microbiome – Justine Dees – ASM

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function – Brittany A. Niccum – mSystems

Bioinformatics

*Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses – Chiara Vanni – bioRxiv

Welcome to the dark side of genomes and metagenomes – a blog post about the above mentioned study – Antonio Fernandez-Guerra

GraphBin: refined binning of metagenomic contigs using assembly graphs – Vijini Mallawaarachchi – Bioinformatics

Podcast

*Reproducible pipelines and NGLess with Luis Pedro Coelho – Roman Cheplyaka – The Bioinformatics Chat

June 22, 2020

General microbiome
Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plants – Robert Heyera – Bioresource Technology

Human microbiome
REVIEW: Role of the Microbiome in Allergic Disease Development – Andrea C. Aguilera, – Pediatric Allergy and Immunology

Optimization and standardization of the culturomics technique for human microbiome exploration – Ami Diakite – Scientific Reports

Human skin microbiome
The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing – J. Travis – BMC Microbiology

Human gut microbiome
Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection – Salma Alavi – Cell

EDITORIAL: Gut microbes effects on host metabolic alterations in health and disease – Suzana D. Savkovic – Gut Microbes

Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study – Mohammad Tahseen Al Bataineh – Scientific Reports

Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma – Yelena Lapidot – mSystems

Human respiratory microbiome
Taxonomic diversity of sputum microbiome in lung cancer patients and its relationship with chromosomal aberrations in blood lymphocytes – V. G. Druzhinin – Scientific Reports

Pregnancy and early life
Human milk microbiota development during lactation and its relation to maternal geographic location and gestational hypertensive status – Yi Wan – Gut Microbes

Maternal Microbiota, Cortisol Concentration, and Post-PartumWeight Recovery Are Dependent on Mode of Delivery – Marta Selma-Royo – Nutrients

Human ancient microbiome
Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia – Anna Philips – BMC Genomics

Animal experiments
Zebrafish microbiome studies make waves – Keaton Stagaman – Lab Animal

Animal microbiome
An Insight into Diversity and Functionalities of Gut Microbiota in Insects – Shengchen Wang – Current Microbiology

Plant, root, and soil microbiome
Microbial assimilation dynamics differs but total mineralization from added root and shoot residues is similar in agricultural Alfisols – Yingde Xu – Soil Biology and Biochemistry

Effects of increasing concentrations of unamended and gypsum modified bauxite residues on soil microbial community functions and structure – A mesocosm study – Camille Fourrier – Ecotoxicology and Environmental Safety

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables – Peter Kusstatscher – FEMS Microbiology Ecology

Variations of rhizospheric soil microbial communities in response to continuous Andrographis paniculata cropping practices – Junren Li – Botanical Studies

Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach – Nima Ranjbar Sistani – Frontiers in Plant Science

Water microbiome
Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates – Hiroaki Takebe – Microbes and Environments

Built environment
MINI-REVIEW: Microorganisms populating the water-related indoor biome – Monika Novak Babič – Applied Microbiology and Biotechnology

Pre-print
Shotgun metagenomics reveals signicant gut microbiome features in different grades of acute pancreatitis – Shanshan Yu – Research Square

Characteristics of Esophagus Flora in Patients with Esophageal Squamous Cell Carcinoma in Central China – Shuixiang He – Research Square

Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb? – Magdalena Wutkowska – bioRxiv

Microbes on the market
Finch Therapeutics Announces Positive Topline Results from Randomized Controlled Trial of CP101, an Oral Microbiome Drug, for the Prevention of Recurrent C. difficile Infection – Finch Therapeutics

Microbes in the news
Gut reaction: How the gut microbiome may influence the severity of COVID-19 – Shirin Moossavi – The Conversation

Towards virtual physiological humans: integrating metabolism, physiology, and gut-microbiome

Science communication on a recently published paper


Precision Medicine

A milestone in precision medicine would be the ability to explore generative models that can capture the real-world complexity of human physiology. If computational models can successfully integrate physiology, metabolism, and host-microbiome data – thereby achieving personalization of predictive models of virtual physiological humans – this would be a key stepping-stone in yielding promising therapeutic targets that are both individual-specific and case-specific. Thus, the science (and art) of generating and exploring virtual physiological humans could be a boon to systems physiology and precision medicine.

Whole-body metabolic reconstructions

Towards this end, Thiele et al. recently published an intriguing paper. Thiele et al. demonstrate building and validation of sex-specific curated Whole-Body Metabolic (WBM) reconstructions. Computational models derived from such WBM reconstructions offer a novel molecular-level, anatomically and physiologically consistent, sex-specific genome-scale reconstructions of human physiology and metabolism. Thiele et al. further demonstrated that the WBM reconstructions can be ‘personalized’ via integration of quantitative physiological data with multi-omics such as metabolomics, and gut-microbiome. Thus, Thiele et al. introduce Harvey and Harvetta, the male and female WBM reconstructions, respectively. These reconstructions and the derived models and analysis enable novel assessment of, e.g., host-microbiome co-metabolism that is individual-specific and is resolved at an organ-level.

Complexity

The extreme complexity of real-world metabolic modelling of host-microbiome in humans can hardly be overstated. Thiele et al. address this critical challenge via constraint-based reconstruction – their models account for the enormous diversity of microbiome-associated microbial genes that are meaningful both physiologically and is individual-specific such as in host-microbiome co-metabolism. Thus this approach allows case-specific investigation of human metabolism, such as for studying inherited metabolic diseases.

Approach

Previously the Thiele Lab , extensive metabolic modelling of metabolic and physiologically relevant pathways (curated algorithmically and manually) led to a comprehensive model that allows investigation via constraint-based reconstruction of over 80,000 pathways. Thiele et al. approached the problem into a smaller sub-problems that they have previously addressed. First – by compiling organ-specific information from previous literature and including experimental-omics data, Thiele Lab generated WBM reconstructions. Second – Thiele Lab imposed constraints the WBM reconstructions via (large-scale) physiology, dietary constraints and quantitative metabolomic data.

Highlights

A key challenge that Thiele et al. addressed in this current 2020 paper is the integration of more than 80,000 biochemical reactions, that were both anatomically and physiologically consistent. These WBM reconstructions describe 26 organs and 6 blood cell types and capture whole-body organ-resolved metabolism. Importantly, these recapitulate previously known inter-organ metabolic cycles and energy use. Interestingly, WBM models can also predict biomarkers. This might, e.g., elucidate new pathways or targets that are implicated in heritable metabolic diseases.

Take-home-message and future ahead

Exploring such quantitative metabolic models could reveal new molecular insights pertaining to (co-dependence of host-microbiome) metabolism and overall human physiology and homeostasis – both in health and disease. The power of computational models is further exemplified if these allow addressing questions via novel hypothesis-testing that go beyond the scope of wet-lab experiments.


written by: Div Prasad

I’m interested in quantitative biology (at the intersection) of human genetics, machine learning, and host-microbiome interactions.

Twitter: @divyaePrasad
github: divprasad

June 5, 2020

Today’s digest features a review on genetic variability within species in microbiomes, a study on Lactobacilli in the human nose, a new episode of Microbiology Lab Pod with the latest science news on functional metagenomics, a novel resistance gene called GAR, and more. Happy reading/listening!

General microbiome

*Diversity within species: interpreting strains in microbiomes – Thea Van Rossum – Nature Reviews

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes – Bin Ma – Microbiome

Oral and nasal microbiome

Local oral and nasal microbiome diversity in age-related macular degeneration – Jacob Rullo – Scientific Reports

*Lactobacilli Have a Niche in the Human Nose – Ilke De Boeck – Cell Reports

Gut microbiome

Resistant maltodextrin intake reduces virulent metabolites in the gut environment: randomized control study in a Japanese cohort – Yuichiro Nishimoto – MedRxiv

Pregnancy and early life

One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces – Ana Paula Christoff – PlosOne

Animal microbiome

Cecal microbiome composition and metabolic function in probiotic treated broilers – Denise R. Rodrigues – PlosOne

Characterization of native Escherichia coli populations from bovine vagina of healthy heifers and cows with postpartum uterine disease – Candelaria Gonzalez Moreno – PlosOne

Animal experiments

Structural and Functional Changes of Gut Microbiota in Ovariectomized Rats and Their Correlations With Altered Bone Mass – Sicong Ma – Aging

Plant, root, and soil microbiome

Dissecting the effect of continuous cropping of potato on soil bacterial communities as revealed by high-throughput sequencing – Jing Zhao – Plos One

Water microbiome

Increasing flow rate reduces biofouling and colonization by filamentous bacteria in drippers fed with reclaimed wastewater – Kevin Lequette – bioRxiv

Phages and viruses

Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage – Priyanka Pandya – PlosOne

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes – Kira Moon – Microbiome

Bioinformatics

Estimating Microbial Interaction Network: Zero-inflated Latent Ising Model Based Approach– Jie Zhou – bioRxiv

Assessment of statistical methods from single cell, bulk RNA-seq and metagenomics applied to microbiome data – Matteo Calgaro – bioRxiv

Metabolomics

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power– Jasmin Hafner – Synthetic Biology

Inferring Active Metabolic Pathways from Proteomics and Essentiality Data – Ariadna Montero-Blay – Cell Reports

Podcast

*May 2020 Pod: Discovering novel resistance genes and how bacteria become virulent – Bengtsson-Palme Lab and Marlies Böhm – Microbiology Lab Pod

June 3, 2020

Today’s post covers articles on role of microbiome in sepsis, early life microbiota related to cystic fibrosis and respiratory syncitial virus disease, promise and challenge with cancer microbiome, effect of probiotics on intestinal homeostasis after chemotherapy and many more!

General microbiome

Predictive biology: modelling, understanding and harnessing microbial complexity – Allison J. Lopatkin – Nature Reviews Microbiology

The Gut Microbiome’s Role in the Development, Maintenance, and Outcomes of Sepsis – Max W Adelman – Critical Care

The Promise and Challenge of Cancer Microbiome Research – Sumeed Syed Manzoor – Genome Biology

Antidiabetic Effects of Flavan-3-ols and Their Microbial Metabolites – Estefanía Márquez Campos – Nutrients

Human microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome – Roie Levy – PNAS

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale – Soumaya Zlitni – Genome Medicine

Comparative Assessment of Faecal Microbial Composition and Metabonome of Swine, Farmers and Human Control – Shiang Chiet Tan – Scientific Reports

Matching Between Donors and Ulcerative Colitis Patients Is Important for Long-Term Maintenance After Fecal Microbiota Transplantation – Koki Okahara – Journal of Clinical Medicine

Preganancy and early life

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure – Min Fu – mBio

Development of the Gut Microbiota in Early Life: The Impact of Cystic Fibrosis and Antibiotic Treatment – Maartje Kristensen – Journal of Cystic Fibrosis

Altered Gut Microbiota in Infants Is Associated With Respiratory Syncytial Virus Disease Severity – Jeffrey N Harding – BMC Microbiology

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth – M A Rasmussen – Isme Journal

Animal experiments

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system – R. A. Dowden – Scientific Reports

Repetitive, Mild Traumatic Brain Injury Results in a Progressive White Matter Pathology, Cognitive Deterioration, and a Transient Gut Microbiota Dysbiosis – Mariana Angoa-Pérez – Scientific Reports

Association of Gut Microbiota Composition and Function With an Aged Rat Model of Senile Osteoporosis Using 16S rRNA and Metagenomic Sequencing Analysis – Sicong Ma – Aging

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function – Yu Pi – mSystems

Plant, root and soil microbiome

Using Soil Bacterial Communities to Predict Physico-Chemical Variables and Soil Quality – Syrie M Hermans – Microbiome

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages – Corinne Biderre-Petit – Fems Microbial Ecology

Water microbiome

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation – Zaisheng Yan – Environmental Microbiology

Functional foods

Effect of Probiotics on the Maintenance of Intestinal Homeostasis After Chemotherapy: Systematic Review and Meta-Analysis of Pre-Clinical Studies – W G Lima – Beneficial Microbes

Non microbiology picks

Racial Disparities in Knowledge, Attitudes and Practices Related to COVID-19 in the USA– Wilson M Alobuia – Journal of Public Health

Ozone Treatment for Elimination of Bacteria and SARS-CoV-2 for Medical Environments – Craig Westover – BioRxiv

May 27, 2020

Good morning everybody. It was a bit calm during the last days. Today’s Microbiome Digest tries to give a nice summary of a broad range of latest microbiome related research. Enjoy it!

General microbiome

A microbiological survey of handwashing sinks in the hospital built environment reveals differences in patient room and healthcare personnel sinks – Franco et al – Scientific Reports

Multi-site human microbiome

REVIEW: Interaction between microbiota and immunity in health and disease – Zheng, Liwinski and Elinav – Cell Research

REVIEW: A Comprehensive Review on Natural Bioactive Compounds and Probiotics as Potential Therapeutics in Food Allergy Treatment – Pratap et al. – Front. Immunol.

Editorial: The intestinal microbiota in health and disease – Day, Keenan and Tannock – Journal of the Royal Society of New Zealand

Human oral microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al. – Scientific Reports

Human skin microbiome

Skin Microbiome in Atopic Dermatitis – Edslev, Agner and Andersen – Acta Dermato-venereologica

Human gut microbiome and virome

Preprint: Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation – Sims et al. – medRxiv

The intestinal virome in children with cystic fibrosis differs from healthy controls – Coffey et al. – PLOS One

The human gut microbiota and depression: widely reviewed, yet poorly understood – Simpson, Schwartz and Simmons – Journal of Affective Disorders

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? – Magne et al. – Nutrients

Book Chapter: Who Inhabits Our Gut? Introducing the Human Gut Microbiota – Flint – Why Gut Microbes Matter

Book Chapter: Variability and Stability of the Human Gut Microbiome – Flint – Why Gut Microbes Matter

Book Chapter: How to Analyse Microbial Communities? – Flint – Why Gut Microbes Matter

Book Chapter: Treating the Gut Microbiome as a System – Flint – Why Gut Microbes Matter

Metabolomics

REVIEW: Application of metabolomics to the study of irritable bowel syndrome – Bennet et al. – Neurogastroenterology & Motility

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

Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse – van de Wouw et al. – Microbiology

Preprint: Physical activity shapes the intestinal microbiome and immunity of healthy mice but has no protective effects against colitis in MUC2-/- mice – Estaki et al. – bioRxiv

Synergetic responses of intestinal microbiota and epithelium to dietary inulin supplementation in pigs – He et al. – European Journal of Nutrition

Animal microbiome (for animals in the wild)

No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus) – Scheelings et al. – Scientific Reports

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea – Ma et al. – The ISME Journal

Plant, root, and soil microbiome

The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts – Zolti et al. – Microbiology

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

16S rRNA Gene Diversity in the Salt Crust of Salar de Uyuni, Bolivia, the World’s Largest Salt Flat – Pecher et al. – Microbiol Resour Announc

Built environment (subways, indoor surfaces)

Fungal diversity and its contribution to the biodeterioration of mural paintings in two 1700-year-old tombs of China – Ma et al. – International Biodeterioration & Biodegradation

Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance – Torralba et al. – Microbial Ecology

Food microbiology

Proteomic and Metabolomic Correlates of Healthy Dietary Patterns: The Framingham Heart Study – Walker et al. – Nutrients

Bioinformatics/Resources

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining – Mungan et al. – Nucleic Acid Research

Draft Genome Sequence of a Novel Species of Halococcus (Strain IIIV-5B), an Endophytic Archaeon Isolated from the Leaf Tissue of Avicennia germinans – Zayas-Rivera et al. – Microbiol Resour Announc

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 – Asnicar et al. – Nature Communications

May 17, 2020

Hello from the Sonoran Desert! It is a sunny Sunday over Tucson, Az! I find that Sundays are the best to explore new ideas and concepts, and I especially love to take the time to read a good opinion piece or parse few review papers. In today’s digest, you’ll find a fascinating review on the Tara Ocean expedition and how it changed our understanding of marine microbial communities. If you’re more interested in the human-associated microbiome, fear not! There is also great pieces on the gut microbiota in athletes and on the interaction of oral and lung microbiome in the context of lung diseases.

If like me, you are a computational biologist thinking about microbiome data all day, you should enjoy reading today’s non microbiology pick, a great perspective paper discussing the FAIR (Findable, Accessible, Interoperable and Reusable) data principle and what are the current hurdles that limit open data reuse.

Have a great Sunday!


Pregnancy and early life

Review: The impact of maternal and early life malnutrition on health: a diet-microbe perspective – Andrew J. Forgie et al. – BMC Medicine

Multi-site human microbiome

Perspective: Microbial Diagnostics for Cancer: A Step Forward but Not Prime Time Yet –  Cynthia L. Sears et al. – Cancer Cell

Human respiratory microbiome

Review: Oral-lung microbiome interactions in lung diseases –  Manoj J. Mammen et al. – Periodontology

Human gut microbiome

Review: The athletic gut microbiota – Alex E. Mohr et al. – Journal of the International Society of Sports Nutrition

Colorectal cancer occurrence and treatment based on changes in intestinal flora – Huifang Si et al. –  Seminars in cancer Biology


Animal experiments 

Microbial communities modulating brain functioning and behaviors in zebrafish: A mechanistic approach – Larica Mohanta et al. –  Microbial Pathogenesis

Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance – Ming-Yuan Xue et al. – Microbiome

Preprint: Rumen protozoa shape microbiome composition and metabolic output of fermentation – Ronnie Solomon et al. – bioRxiv

Animal microbiome (for animals in the wild)

Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development – Zhongwei Yin et al. – Microbiology

After the bite: bacterial transmission from grey seals (Halichoerus grypus) to harbour porpoises (Phocoena phocoena) – Maarten J. Gilbert et al. – Royal Society open science

Exploration of the virome of the European brown shrimp (Crangon crangon) – Benigna Van Eynde et al. – Journal of General Virology

Plant, root, and soil microbiome

Opinion: The Role of Rhizosphere Bacteriophages in Plant Health – Akbar Adjie Pratama et al. – Trends in Microbiology

Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing –  Li Chen et al. – PeerJ

Shifts of bacterial community structure and function in long-term soybean monoculture – Fengjuan Pan et al. – Archives of Agronomy and Soil Science

Bacterial Diversity in Peat Soils of Forest Ecosystems and Oil Palm Plantation – N. A. Kusai et al. – Soil Biology

Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale – Kaoping Zhang et al. – mSystems

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

Competition for iron drives phytopathogen control by natural rhizosphere microbiomes – Shaohua Gu et al. – Nature Microbiology

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

Review: Tara Oceans: towards global ocean ecosystems biology – Shinichi Sunagawa et al. – Nature Reviews Microbiology

Review: Microbial genomics amidst the Arctic crisis – Arwyn Edwards et al. – Microbial genomics

Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes – Marlène Chiarello et al. – Proceedings of the royal society biological sciences


Bioinformatics

A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals – Hyunwook Koh et al. – Microbiome

Review: A practical guide to amplicon and metagenomic analysis of microbiome data – Yong-Xin Liu et al. – Protein Cell

TAMA: improved metagenomic sequence classification through meta-analysis – Mikang Sim et al. – BMC Bioinformatics

nf-rnaSeqMetagen: A nextflow metagenomics pipeline for identifying and characterizing microbial sequences from RNA-seq data – Phelelani T. Mpangase et al. – Medicine in Microecology


My non-microbiology pick

Perspective: FAIR Data Sharing: The Roles of Common Data Elements and Harmonization – R.D.Kush et al. – Journal of Biomedical Informatics

Probiotics to precision probiotics

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 8, 2020.

The highlighted paper of the day looked at the relationship between statins and gut microbiome / enterotype prevalence, mined from data collected from the MetaCardis study which looked at over 2000 participants all across the EU and collected over 1,400 parameters.

If you’re looking for a review/news article of the paper head to: Statin drugs might boost healthy gut microbes

If you’re looking for the paper: Statin therapy is associated with lower prevalence of gut microbiota dysbiosis – Sara Silva – Nature

COVID-19


Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids – Xiaohua Duan – bioRxiv

Whose coronavirus strategy worked best? Scientists hunt most effective policies – Elizabeth Gibney – Nature

Coronavirus activates a stem cell-mediated defense mechanism that accelerates the activation of dormant tuberculosis: implications for the COVID-19 pandemic – Lekhika Pathak – bioRxiv

General Microbiome

Multi ‘Omics Profiling of the HIV Airway Epithelium: Integration of the Microbiome, Methylome, and Transcriptome – MS Jude – Am J Respir Crit Care Med

Intracellular Staphylococcus aureus persisters upon antibiotic exposure – Frederuc Peyrusson – Nature Communications

Isolation and characterization of bacteriophages that infect Citrobacter rodentium, a model pathogen for investigating human intestinal diseases – Carolina Mizuno – bioRxiv

MiniReview: A toxic environment: a growing understanding of how microbial communities affect Shiga toxin expression by E. coli O157:H7 – Erin M. Nawrocki – American Society for Microbiology, Applied and Environmental Microbiology

Pregnancy and early life

Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to- weaning transition – Martin Beaumont – Gut Microbes

Gut Microbiome Derived 12,13 Dihome Promotes Antigen Presenting Cell Dysfunction In Vitro and Airway Allergic Inflammation In Vivo – S Levan – Atsjournal


Multi-site human microbiome

The Microbiome and the Gut‐Liver‐Brain Axis for CNS Clinical Pharmacology: Challenges in Specifying and Integrating In Vitro and In Silico Models – Kyle Hawkins – Clinical Pharmacology and Therapeutics

Gut Check: The Intestinal Microbiome Does Not Predict or Protect from Vancomycin- Resistant Enterococcus Acquisition Among Critically Ill Patients – Chanderraj – Atsjournal

The Tumour-Resident Microbiome Is Associated with Cancer Hypomethylation Status in Lung Adenocarcinoma – Marshall – atsjournal

An association between the gut microbiota and immune cell dynamics in humans. – Jonas Schluter – bioRxiv

Metabolomics

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics – Vrieling Frank

Review: Metabolome–Microbiome Crosstalk and Human Disease – Kathleen Lee-Sarwar – metabolites

Animal Microbiome

Review – Mycobacterium bovis: From Genotyping to Genome Sequencing – Ana Guimaraeas – Microorganism

Animal experiments

Staphylococcus aureus-induced proteomic changes in the mammary tissue of rats: A TMT-based study – Lirong Cai – Plos One

Plant, root, and soil microbiome


Effects of earthworms on the microbiomes and antibiotic resistomes of detritus fauna and phyllosphere – Dong Zhu – Environmental Science and Technology

Surface runoff alters cave microbial community structure and function – Madison Davis – Plos One

Water and extremophile microbiome

Culturing of ‘Unculturable’ Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater – Xiaoqin Wu – bioRxiv

Bioinformatics & Techniques

Sequence count data are poorly fit by the negative binomial distribution – Stjin Hawinkel – Plos One

Book Chappter: Meta-Pangenome: At the Crossroad of Pangenomics and Metagenomics – Bing MA – The Pangenome, Springer.

Snipe: Highly sensitive pathogen detection from metagenomic sequencing data – Lihong Huang – bioRxiv

Validated Method for the Study of Human Lung Microbiota from Excised Tissue – Dumont-Leblond – atsjounal

Microbes in the news

Bad to the Bone – Matthew Greseth- MUSC Health

Meet the ‘psychobiome’: the gut bacteria that may alter how you think, feel, and act – Elizabeth Pennisi – ScienceMag

Decoding the Microbiome: Essential to Advancing Precision Medicine – Heather Hall – rdworldonline

Harithaa’s non-microbiology picks!

Mass spectrometry for future atomic clocks – Marianna Safrova – Nature (news & views)

May 2nd, 2020

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!