February 27th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in gut microbiomes, I recomment taking a look at the preprint by Weiss and collaborator. In this study, they explore bacteria-bacteria interactions, bacterial growth and metabolic interactions in a synthetic bacterial community: the Oligo-Mouse-Microbiota, which is increasingly used as model system in gut microbiome research.

Additionally, anyone interested in microbiome-based forensic tools should read the study from Sang You and collaborators.  They compared the composition of microbial communities in blood spot surfaces placed in different environments sampled across seasons and time points, in order to evaluate the environmental factors leading to variation in these microbial communities.

Today’s non-microbiology pick is a fascinating study looking at the prevalence of COVID-19 related misinformation among the Yemeni population and its association with vaccine acceptance and perceptions. From this study, the authors recommend the deployment of awareness campaigns to decrease misinformation before initiating any mass vaccination in Yemen.

Have a great Weekend!


Human gut microbiome

Review: The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling – Gangadoo et al. – International Journal of Molecular Sciences

Preprint: Exploring the interaction network of a synthetic gut bacterial community – Weiss et al. – BioRxiV


Animal experiments

Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions – Rehman Kayani et al. – Environmental Pollution

Fish farm effluents as a source of antibiotic resistance gene dissemination on Jeju Island, South Korea – Jo et al. – Environmental Pollution

Influence of environmental factors and bacterial community diversity in pond water on health of Chinese perch through Gut Microbiota change – Li et al. – Aquaculture Reports

Preprint: The diversity, composition, and metabolic pathways of archaea in pigs – Deng et al. – Preprints

Animal microbiome

Preprint: Stony Coral Tissue Loss Disease biomarker bacteria identified in corals and overlying waters using a rapid field-based sequencing approach – Becker et al. – bioRxiV

Built environment

Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions – Sang You et al – FEMS Microbiology letters


Phages and viruses

Opinion paper: Rapid emergence of virus–host mutualism under stress – Dolja – PNAS

Patterns of virus growth across the diversity of life – Jin and Yin – Integrative biology

Techniques

Standard Bacteriophage Purification Procedures Cause Loss in Numbers and Activity – Carroll-Portillo et al. – Viruses


My non-microbiology picks

Preprint: Misinformation, Perceptions Towards COVID-19 and Willingness to be Vaccinated: A Population-Based Survey in Yemen – Naoras Bitar et al. – BioRxiV

January 24, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in  early-life microbiome, I recommend taking a look at the paper from Mortensen and collaborators. To understand the role of the maternal vaginal microbiome’s in seeding their child and the importance of the delivery mode in early-life microbiome acquisition, they studied 665 mother–child dyads and modeled the transfer of the vaginal microbiota from mother to infants.

In today’s digest, you’ll also find a really interesting preprint from Abiriga and collaborators, looking at the microbiome of a groundwater aquifer contaminated by a municipal landfill while undergoing intrinsic bioremediation. This preprint is particularly notable because studies looking at the microbiome of contaminated aquifers are particularly rare, despite groundwater contaminations from landfills being a very common issue.

Today’s non-microbiology pick takes a look at the difficulty of detecting scientificly fraudulent images produced by Generative Adversarial Networks (GANs). They demonstrate that this deep-learning method can generate realistic western blot images that are indistinguishable from real western blots. In conclusion, the authors argues that additional information should be required to ensure that the western blots published in scientific publication are not generated images. 

Have a great Sunday!


Human respiratory microbiome

Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism – Sulaiman et al. – European respiratory journal

Human skin microbiome

Preprint: Comparative investigation of the Diabetic foot ulcer microbiome – Saeb et al. – BioRxiv

Human vaginal microbiome

Preprint: Vaginal bacterial load in the second trimester is associated with early preterm birth recurrence: a nested case-control – Goodfellow et al. – MedRxiv

Modeling transfer of vaginal microbiota from mother to infant in early life – Mortensen et al. – eLife

Human gut microbiome

Review: Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations – Lamichhane et al. – Metabolites


Animal microbiome

Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus) – Funosas et al. – Scientific reports

Plant, root, and soil microbiome

Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic – Varsadiya et al. – FEMS Microbial ecology

Book chapter: Microbial Diversity of Phyllosphere – Dhankhar et al. – Phytomicrobiome Interactions and Sustainable Agriculture

Review: Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome – Singer et al. – Phytomes journal

Water and extremophile microbiome

Book chapter: Potential of Extremophiles for Bioremediation – Kaushik et al. – Microbial Rejuvenation of Polluted Environment. Microorganisms for Sustainability, vol 25. Springer, Singapore.

Built environment

Microbial Diversity Analysis of Sediment from Yeosu New Harbor of South Korea Using 16S rRNA Gene Amplicon Sequencing – Lee et al. – Microbiology ressource announcements

Preprint: Characterisation of the bacterial microbiota of a landfill-contaminated confined aquifer undergoing intrinsic remediation – Abiriga et al. – BioRxiv


Phages and viruses

Reduced metagenomic sequencing (RMS) approach to determine the gut-associated phageome in mother-child – Manohar et al. – Human Microbiome Journal

Review: Enteric Viruses and Inflammatory Bowel Disease – Tarris et al. – Viruses

Bioinformatics

book chapter: Advances in Omics and Bioinformatics Tools for Phyllosphere Studies – Bansal – Phytomicrobiome Interactions and Sustainable Agriculture

MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning – Dhungel et al. – BMC Bioinformatics


My non-microbiology picks

Preprint: Emerging Concern of Scientific Fraud: Deep Learning and Image Manipulation – Qi et al. – BioRxiv

December 27, 2020

Joyeuses fêtes from Paris, France ! In today’s digest, you will find great papers looking at various animal and plant microbiomes. In particular, I recommend taking some time to look at a preprint from Brealey and collaborators exploring the impact of human antibiotic use on oral microbiome in wild animals. The authors used shotgun metagenomics to determine the abundance and diversity of antimicrobial resistance genes in the oral microbiome of brown bears from Swedish museum specimens. Importantly, they show a significant increase in antimicrobial resistance genes in correlation with modern human antibiotics use, showing an impact even on wildlife of our antibiotic consumption.

Today’s non-microbiology pick takes a look back at the history of bioinformatics through the data analysis and visualization of papers published between 1998 and 2019. In addition of reading this very interesting paper, you can take a look at the data collected through interactive visualizations available at http://bioinfo.dcc.ufmg.br/history !

Have a great Sunday!


Pregnancy and early life

Preprint: Metabolomic signature of the maternal microbiota in the fetus – Pessa-Morikawa et al. – BioRXiv

Human nearly-sterile sites

Preprint: The urinary microbiome in postmenopausal women with recurrent urinary tract infections – Hiersoux Vaughan et al. – BioRXiv

Preprint: Biofilm development on urinary catheters promotes the appearance of viable but non-culturable (VBNC) bacteria – Wilks et al. – BioRXiv


Animal microbiome

Preprint: Wild animal oral microbiomes reflect the history of human antibiotics use – Brealey et al. – BioRXiV

Plant, root, and soil microbiome

Dissimilarity analysis of microbial communities in the rhizosphere and tissues of diseased and healthy cherry trees (Cerasus pseudocerasus) – Ding et al. – Canadian Journal of Plant Pathology

First Recorded Account of Arbuscular Mycorrhizal Fungi in Sand Dunes in South Eastern Australia: Biogeography and Species Richness – Hanlon et al. – Journal of Coastal Research

Diversity and structural differences of bacterial microbial communities in rhizocompartments of desert leguminous plants – Zhou et al. – PLOS ONE

Preprint: Orchard management and landscape context mediate the floral microbiome of pear – Schaeffer et al. – BioRXiv

Water and extremophile microbiome

Interplay of microbial communities with mineral environments incoralline algae – Valdespino-Castillo et al. – Science of the total environment

Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain – Chacon-Baca et al. – Astrobiology


Bioinformatics

PStrain: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data – Wang et al. – Bioinformatics

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data – Leung et al. – BMC Genomics


My non-microbiology picks

A Brief History of Bioinformatics Told by Data Visualization – Mariano et al. – Brazilian Symposium on Bioinformatics

 

December 17, 2020

Bonjour from Paris, France ! In today’s digest, readers interested in viromes will find a nice selection of papers looking at the viral populations associated to deep lake waters, birds, star fish and human gut! I also recommend anyone interested in this topic to take a look at a preprint from Amgarten and collaborators presenting a new computational tool called “vHULK”, allowing an in-silico bacteriophage host prediction!

Readers may also be interested in taking a look at the announcement of a new web interface allowing the exploration of the Human Microbiome Project (HMP). The ressource, called HMPDACC, provides a unified data repository for the two phases of the HMP, allows to search samples on a multitude of metadata, and provides analysis pipelines and standardized protocols to facilitate community use of HMP dataset.

Finally, today’s non-microbiology digest is a paper taking a look at the avalanche of papers and preprints published this year around the COVID-19 pandemic. Impressively, 84,180 indexed publications were relevant to COVID-19 written by 322,279 unique authors from all scientific subfields (except for Automobile Design & Engineering scientists!)

Have a great Saturday!


General microbiome

Preprint: Trait Evolution in Microbial Communities – Zhao et al. – BioRXiv

Human gut microbiome

The Pre‐treatment Gut Microbiome is Associated with Lack of Response to Methotrexate in New Onset Rheumatoid Arthritis – Artacho et al. – Arthitis and Rheumatology

Chapter: Oral Microbes: A Hidden Yet Powerful Evidence for Futuristic Forensic Investigation – Patel and Ganguly Soni – In: Shrivastava P., et al. (eds) Forensic DNA Typing: Principles, Applications and Advancements. Springer.

Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank – Wirth et al. – Cancers


Animal microbiome

Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea – Oliveira et al. – mircoorganisms


Phages and viruses

Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery – Truchado et al. – microorganisms

Virome Analysis of Near-Bottom Coastal Water of Lake Baikal – Butina et al. – Microbiology ressource announcements

Virome Variation during Sea Star Wasting Disease Progression in Pisaster ochraceus (Asteroidea, Echinodermata) – Hewson et al. – Viruses

Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger? – Massimino et al. – Computational and structural biotechnology journal

Bioinformatics

Preprint: vHULK, a new tool for bacteriophage host prediction based on annotated genomic features and deep neural networks – Amgarten et al. – BioRXiv

HMPDACC: a Human Microbiome Project Multi-omic data resource – Huot Creasy et al. Nucleic Acids Research

Review: Literature on Applied Machine Learning in Metagenomic Classification: A Scoping Review – Tonkovic et al. – biology


My non-microbiology picks

Preprint: The rapid, massive infection of the scientific literature and authors by COVID-19 – Ioannidis et al. – BioRXiv

November 14, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find great papers, in particular in soil and water microbiology but also in bioinformatics! As an example, Mara and collaborators are exploring the viruses found in the oxygen-deficient water column of the Cariaco basin. Interestingly, a large diversity of viral Auxilliary Metabolic Genes (AMGs) were found and give new insights in how phages may interact with their bacterial hosts in this understudied ecosystem.

In the bioinformatics section, I recommend anyone interested in phage metagenomics to take a look at the paper from Ren and collaborators. The authors have developed a reference-free and alignment-free deep learning tool, called DeepVirFinder, allowing the retrieval of viral sequences in metagenomes.

Today’s non-microbiology digest is a paper announcing the last update of the Genome Online Database (GOLD), a manually curated collection of genome projects and their metadata from around the world, which now contains more than a million entries! Great news for bioinformaticians!

Have a great Saturday!


Human gut microbiome

The bacterial association with oral cavity and intra-abdominal abscess after gastrectomy – Nishikawa et al. – PlosOne


Animal microbiome

Loss of symbiont infectivity following thermal stress can be a factor limiting recovery from bleaching in cnidarians – Kishimoto et al. – ISME Journal

Plant, root, and soil microbiome

A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases – Tian et al. – ISME Journal

Air microbiome

Spatio-temporal variations in bacterial and fungal community associated with dust aerosol in Kuwait – Al Salameen et al. – PlosOne

Water and extremophile microbiome

Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system – Huber et al. – ISME Journal

A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities – Kraemer et al. – ISME Journal

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline – Mara et al. – ISME Journal


Phages and Viruses

Metagenomic Analysis of the Enteric RNA Virome ofInfants from the Oukasie Clinic, North West Province,South Africa, Reveals Diverse Eukaryotic Viruses – Mogotsi et al. – Viruses

Bioinformatics

Identifying viruses from metagenomic data using deep learning – Ren et al. – Quantitative Biology

Review: Reconstructing organisms in silico: genome-scale models and their emerging applications – Fang et al. – Nature Reviews Microbiology

Zero-Inflated gaussian mixed models for analyzing longitudinal microbiome data – Zhang et al. – PlosOne

Evaluating the number of different genomes in a metagenome by means of the compositional spectra approach – Kirzhner et al. – PlosOne

Survey of metaproteomics software tools for functional microbiome analysis – Sajulga et al. – PlosOne

Techniques

Sample pooling methods for efficient pathogen screening: Practical implications – Furstenau et al. – PlosOne


My non-microbiology picks

Genomes OnLine Database (GOLD) v.8: overview and updates – Mukherjee et al. – Nucleic Acids Research

November 1, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find several interesting works, in particular on recent advances in understanding the gut microbiome! Iandaza and collaborators review the rise of machine learning and deep learning methods in exploring the gut microbiota and the potential of these methods in the diagnosis and treatment of diseases. Additionally, this digest links to a freely-accessible webinar series from the university of Illinois on gut-brain connections.

If you are interested in microbial ecology, I also recommend taking a look at a very interesting preprint from Ettinger and collaborators. The authors investigate the distribution of fungi associated with a widely distributed seagrass, Zostera marina. This work is particularly relevant since the role and diversity of fungi in marine ecosystems are often overlooked in microbiome studies, while terrestrial fungi have been shown to have critical roles as decomposers, pathogens and endophytes.

Finally, you’ll find in this digest a non-microbiology pick: an amazing preprint where authors assessed 2.75 million open access articles on their transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures and protocol registration)!

Have a great Sunday!


Events and webinars

Webinar: Scientific Webinars on the Gut-Brain Connection Spotlight Spike in Research


Pregnancy and early life

Review: The dark matter of microbiome: the mother-infant pair virome – Comitini et al. – Minerva Pediatrica

Human vaginal microbiome

Intrauterine Growth Restriction Is Associated with Unique Features of the Reproductive Microbiome – Hu et al. – Reproductive sciences

Human gut microbiome

Review: Gut microbiota and artificial intelligence approaches: A scoping review – Iadanza et al. – Health and Technology

Review: Circadian rhythms and the gut microbiota: from the metabolic syndrome to cancer – Bishehsari et al. – Nature Reviews Endocrinology

Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut – Nishiyama et al. – Microorganisms


Animal microbiome

Preprint: Genomic and microscopic evidence of stable high density and maternally inherited Wolbachia infections in Anopheles mosquitoes – Walker et al. – BioRxiV

Plant, root, and soil microbiome

Testosterone amendment alters metabolite profiles of the soil microbial community – Ding et al. – Environmental Pollution

Host population size is linked to orchid mycorrhizal fungal communities in roots and soil, which are shaped by microenvironment – Kaur et al. – Mycorrhiza

Root exudates drive soil‐microbe‐nutrient feedbacks in response to plant growth – Zhao et al. – Plant, Cell & Environment

Microbial activity and metamitron degrading microbial communities differ between soil and water-sediment systems – Wang et al. – Journal of hazardous materials

Water and extremophile microbiome

Review: Insights into ‘Symbiodiniaceae phycosphere’ in a coral holobiont – Guedes Garrido et al. – Symbiosis

Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice – Juhmani et al. – Microorganisms

Preprint: Global diversity and biogeography of the Zostera marina mycobiome – Ettinger et al. – BioRxiV

Built environment

Analysis of Microbial Community Structure and Diversity in Surrounding Rock Soil of Different Waste Dump Sites in Fushun Western Opencast Mine – Jiang et al. – Chemosphere


My non-microbiology picks

Preprint: Assessment of transparency indicators across the biomedical literature: how open is open? – Serghiou et al. – BioRxiV

October 11, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting reads about ancient microbes!

Duchêne and collaborators review recents efforts in paleopathology leading to the genome sequencing of ancient pathogens of historical interest such as the pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae). In their review, the authors explore this amazing topic that aims to broaden our understanding of the past infectious disease.

On the other hand, Eisenhofer and collaborators examine ancient microbial DNA preserved within dental calculus samples from two major cultural periods in Japan: the Jomon period circa 3000 years ago and the Edo period circa 400–150 ago. In this piece, they explore how human oral microbiomes have changed through time in ancient Japanese populations.

Finally, you’ll find in this digest a non-microbiology pick: a “10 simple rules” paper outlining best practices for annotating and submitting sequencing data! Indeed, metadata accompanying sequence datasets is critical to ensure data longevity and reusability by both human and machine agents, and poor metadata can drastically reduce the value of sequencing experiments by limiting its reuse in integrative analyses!

Have a great Sunday!


General Microbiology

Review: The Recovery, Interpretation and Use of Ancient Pathogen Genomes – Duchêne et al. – Current Biology

Multi-site human microbiome

Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus – Jacobson et al. – Philosphical transactions of the royal society of Biological sciences.

Human respiratory and oral microbiome

Investigating the demographic history of Japan using ancient oral microbiota – Eisenhofer et al. – Philosphical transactions of the royal society of Biological sciences.

Human gut microbiome

Preprint: Distinct human gut microbial taxonomic signatures uncovered with different sample processing and microbial cell disruption methods for metaproteomic analysis – Garcia-Duran et al. – BioRxiv.

Review: Deciphering diet-gut microbiota-host interplay: Investigations of pectin. – Tan and Nie – Trends in Food Science & Technology


Plant, root, and soil microbiome

Book Chapter: Microbes and Environment: Global Warming Reverting the Frozen Zombies. In: Fahad et al. (eds) Environment, Climate, Plant and Vegetation Growth. Springer, Cham.

Taxonomic Diversity of Bacteria and Their Filterable Forms in the Soils of Eastern Antarctica (Larsemann Hills and Bunger Hills) – Kudinova et al. – Microbiology.

Preprint: Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in Icelandic tundra – Klarenberg et al. – bioRxiv

Water and extremophile microbiome

Diversity of Eukaryotic Microorganisms in the Drainage Waters of a Coal Open-Cast Mine – Gruzdev et al. – Microbiology

Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system – Zeng et al. – AMB express.

Comparative diversity analysis of halophiles at two polar saltern systems in Indramayu, West Java, Indonesia – Chasanah et al. – Letters in Applied Microbiology.

Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria – Norris et al. – BioRxiv.

Food microbiology

Review: Microbial diversity of seafood. Parlapani. Current Opinion in Food Science.


Phages and viruses

The first head‐tailed virus, MFTV1, produced by a hyperthermophilic methanogenic deep‐sea archaea – Thiroux et al. – Environmental microbiology.

Review: Single-virus genomics and beyond – Martinez et al. – Nature reviews Microbiology

Bioinformatics

A Rapid Automated Process for Organizing Bacterial Cluster Segments Using Deep Neural Networks – Elroy Martis et al. – IEEE conference

Techniques

FACS-iChip: a high-efficiency iChip system for microbial ‘dark matter’ mining – Liu et al. – Marine Life Science and Technology

Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses – Sabatier et al. – Microorganisms


Science, publishing, and career

Preprint: Advancing science or advancing careers? Researchers’ opinions on success indicators – Aubert Bonn and Pinxten – BioRxiv.

My non-microbiology picks

Ten simple rules for annotating sequencing experiments – Stevens et al. – Plos Computational Biology

September 13, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting reads! In particular, Stepanauskas and collaborators looked at horizontal gene transfer in marine bacterial genomes in a fascinating preprint. They show that marine microorganisms form “gene exchange networks” within which organisms are able to exchange both flexible and core genes, including genes from the rRNA operon! The authors suggest a new definition of microbial species, broader than the current accepted delineation.

Today’s digest also includes few new papers and proceedings presenting novel bioinformatic tools and methods. Among them, Podlevsky and collaborators presents CasCollect, a novel computational tool allowing the assembly and annotation of Cas genes and CRISPR arrays from metagenomic datasets.

Finally, today’s non-biology piece is a very interesting review on the challenge of Big Data in biology: how modern computational frameworks can enable the storage, transfer, access, and analysis of both unstructured and structured massive biological datasets?

Have a great Sunday!


Human vaginal microbiome

Altered vaginal microbiome and relative co-abundance network in pregnant women with penicillin allergy – Li et al. – Allergy , Asthma & Clinical Immunology

Human gut microbiome

Review: Mechanisms underpinning the efficacy of faecal microbiota transplantation in treating gastrointestinal disease – Segal et al. – Therapeutic Advances in Gastroenterology


Animal microbiome

Preprint: Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts – Uecker et al. – BioRxiV

Metagenomic analysis of viral communities in Baikal sponges – Butina and Bukin – Limnology and Freshwater Biology

Microbial community associated with Baicalian crustacea near gas-oil deepwater discharges – Khalzov et al. – Limnology and freshwater biology

Plant, root, and soil microbiome

Preprint: Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana root microbiome – Worsley et al. – BioRxiV

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

Preprint: Gene exchange networks define species-like units in marine prokaryotes – Stepanauskas et al. – BioRxiV

Preprint: The effects of seasonal anoxia on the microbial community structure in demosponges in a marine lake (Lough Hyne, Ireland) – Schuster et al. – BioRxiV

Food microbiology

Preprint: Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine – Liu et al. – BioRxiV


Phages and viruses

Depicting the RNA Virome of Hematophagous Arthropods from Belgrade, Serbia – Stanojevic et al. – Viruses

Preprint: An Unconventional Flavivirus and other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome – Hewson et al. – preprints

Bioinformatics

Review: Challenges in gene-oriented approaches for pangenome content discovery – Bonnici et al. – Briefings in Bioinformatics

Conference proceedings: A Data Driven Binning Method to Recover More Nucleotide Sequences of Species in a Metagenome – Vimukti et al. – IEEE

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data – Podlevsky et al – NAR Genomics and bioinformatics

Techniques

book: Metagenomics: Techniques, Applications, Challenges and Opportunities – Singh et al – Springer Nature Singapore Pte Ltd.


My non-microbiology pick

Review: Big data in biology: The hope and present-day challenges in it Pal et al. – Gene reports

August 23, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting papers! For those interested in soil microbiology, you’ll find in today’s digest a very interesting piece on the the biodiversity and ecology of protists in the soils of the McMurdo Dry Valleys (Antarctica). This piece is particularly exciting given that the role and impact of protists in polar regions is largely unknown and understudied.

Curious readers should also take a look at the amazing study by Dunaj and collaborators focusing on spider’s associated microbiome. This piece examines the host-microbe co-evolution of different widow spider species showing a strong congruence of the microbiome beta-diversity and the host phylogeny.

Finally, in today’s non-microbiology pick, I recommend a preprint, that explored the relationship between the use of jargon and citations in cave research articles. Interestingly the authors suggest that the juse of jargon in title and abstract significantly reduces the number of citations a paper recieves!

Have a great Sunday!


Human vaginal microbiome

Review: The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing – Martina Odogwy et al. – PeerJ

Human gut microbiome

Review: Association or Causation? Exploring the Oral Microbiome and Cancer Links – Teles et al. – Journal of Dental research


Animal microbiome

Learning machine approach reveals microbial signatures of diet and sex in dog – Scarsella et al.- Plos One

Spider phylosymbiosis: divergence of widow spider species and their tissues’ microbiomes – Dunaj et al. – BMC Evolutionary Biology

Plant, root, and soil microbiome

Review: The rhizosphere microbiome: functions, dynamics, and role in plant protection – Rabelo de Faria et al. – Tropical Plant Pathology

Review: The Floral Microbiome: Plant, Pollinator, and Microbial Perspectives – Vannette – Annual review of Ecology, Evolution and systematics

Response of soil microbial communities to natural and managed vegetation restoration in a subtropical karst region – Hu et al. – CATENA

Water and extremophile microbiome

Shotgun metagenomics reveal a diverse assemblage of protists in a model Antarctic soil ecosystem – Thompson et al.- Envirmental Microbiology


Phages and viruses

Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase – Krupovic et al. – Virus Evolution

Bioinformatics

Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach – Reiman et al.- Methods in Molecular Biology, vol 2190. Humana, New York, NY.

Database limitations for studying the human gut microbiome – Dias et al. – PeerJ

Techniques

Review: Microbial High Throughput Phenomics: The Potential of an Irreplaceable Omics – Acin-Albiac et al. – Computational and Structural Biotechnolgy Journal


My non-microbiology pick

Preprint: Specialized terminology limits the reach of new scientific knowledge – Martinez et al. – BioRxiv

July 19, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find find a lot of very interesting papers! For those interested in host-phages interactions, there is an amazing work from Ping and collaborators looking at phage infections dynamics in migrating bacterial populations. Interestingly, the authors suggests that phages may be able to “hitchhike” with moving bacteria.

To continue with our viral readings, you’ll also find an interesting perspective paper from Kuprovic and collaborators. In this piece, the authors attempt to reconstruct the virome associated to LUCA (Last Universal Cellular Ancestor). Amazingly, their reconstruction shows that a remarkably complex virome would have been associated to LUCA, suggesting an extensive viral evolution antedating LUCA!

Finally, today’s non-microbiology pick is a book, looking at the fascinating Cuatro Ciénegas Basin, located in México, a site that is often described as a real outdoor laboratory for astrobiology. Indeed, the Basin site contains gypsum-rich soil analogous to the Gale Crater in Mars, and the ponds contains extremely oligotrophic waters, which can be used to model ancient oceans chemistry. You’ll explore along the chapters the history, ecology, microbiology and evolution of this amazing site, to unravel the mysteries of this site absolutely unique on the planet.

Have a great Sunday!


Human respiratory microbiome

Review: Insights gained into respiratory infection pathogenesis using lung tissue metabolomics –  Bernatchez and McCall –  PLOS Pathogens

Human gut microbiome

Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study –  Van Gompel et al. –  Environment International

Review: The influence of the gut microbiome on obesity –  Blanco – Journal of the American Association of Nurse Practitioners


Animal microbiome (for animals in the wild)

Comparative analysis of the gut microbiota of Apis cerana in Yunnan using high-throughput sequencing. –  Luo et al. –  Archives of Microbiology

Plant, root, and soil microbiome

Higher tree diversity increases soil microbial resistance to drought. –  Gillespie et al. –  Communications Biology

Effect of land uses on soil microbial community structures among different soil depths in northeastern China. –  Ji et al. –  European Journal of soil Biology

Structural variability and niche differentiation of the rhizosphere and endosphere fungal microbiome of Casuarina equisetifolia at different ages. –  Huang et al. –  Environmental Microbiology

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

Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming. –  Zheng et al. –  Nature communications

Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. –  Arsenieff et al.  –  The ISME Journal

Lake characteristics influence how methanogens in littoral sediments respond to terrestrial litter inputs. –  Yakimovich et al. –  The ISME Journal

Built environment (subways, indoor surfaces)

Heavy metal concentrations in Brazilian port areas and their relationships with microorganisms: can pollution in these areas change the microbial community? –  Del Busso Zampieri et al. –  Environmental Monitoring and Assessment

Food microbiology

Material conversion, microbial community composition and metabolic functional succession during green soybean hull composting. –  Zhang et al. –  Bioresource Technology


Phages and viruses

Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. –  Ping et al. – The ISME Journal

Review: The LUCA and its complex virome. –  Krupovic et al. –  Nature Review Microbiology

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. –  Jarett et al. –  ISME Journal

Bioinformatics

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data. –  Rahman and Rangwala –  Bioinformatics


My non-microbiology pick

Book: Astrobiology and Cuatro Ciénegas Basin as an Analog of Early Earth. –  Medina-Chávez et al. –  Cuatro Ciénegas Basin: An Endangered Hyperdiverse Oasis. Springer