February 25th, 2023

Posted on February 25, 2023 by Alise Ponsero

Bonjour from Paris, France !

In today’s digest you will find a broad range of amazing preprints and published papers! Fontana and collaborator performed a fascinating meta-analysis of publicly datasets obtained from fecal samples of healthy athletes and healthy sedentary adults and revealed the microbiota changes associated with competitive athletes lifestyle.

Today’s non-microbiology pick is an preprint exploring postdoctoral and PhD student’s career self-efficacy in US biological sciences and showed how women and non US citizen have a significant lower level of career self-efficacy compared to their male and US citizen peers. The authors discuss potential causes for these differences and offer recommendations for increasing trainee career self-efficacy.

Have a great Saturday!

Pregnancy and early life

Preprint: Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Li et al. – BioRXiv

Human gut microbiome

The human gut microbiome of athletes: metagenomic and metabolic insights – Fontana et al. – Microbiome

Review: Gut microbiome-based strategies for host health and disease – Wang et al. – Critical Reviews in Food Science and Nutrition

The role of diet in shaping human gut microbiota – Rinninella et al. – Best practive & Research clinical Gastroenterology

Preprint: Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria – Robitaille et al. – BioRXiv

Genetic-Phenotype Analysis of Bifidobacterium bifidum and Its Glycoside Hydrolase Gene Distribution at Different Age Groups – Wei et al. – Foods

Animal microbiome

Preprint: Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) – Andres et al. – BioRXiv

Plant, root, and soil microbiome

Preprint: Short- and long-term effects of continuous compost amendment on soil microbiome community – Kraut-Cohen et al. – BioRXiv

Awaking the Dormant Virome in the Rhizosphere – Braga and Schumacher – Molecular ecology

Water and extremophile microbiome

Preprint: A novel order-level lineage of ammonia-oxidizing Thaumarchaeota is widespread in marine and terrestrial environments – Zheng et al. – BioRXiv

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics – Dart et al. – Viruses

Food microbiology

Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica) – Hines et al. – Plos One

Phages and viruses

Review: The Role of Temperate Phages in Bacterial Pathogenicity – Gummalla et al. – Microorganisms

Bioinformatics

Review: Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses – Ibanez-Lligona et al – Viruses

Non microbiology pick

Preprint: Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States – Chatterjee et al. – BioRXiv

February 18th, 2023

Posted on February 18, 2023 by Alise Ponsero

Bonjour from Paris, France !

In today’s digest you will find a broad range of amazing preprints and published papers! An amazing read is a fresh preprint from Fritz and collaborator describing an exciting method of sampling in difficult to reach environments. The authors used army ants of the genus Dorylus which are foragers to survey the viral diversity of plants, vertebrate and invertebrates of the tropical forest!

Today’s non-microbiology pick is an opinion piece on the current state and limitation of viral taxonomy. In this piece, Simmonds and collaborators, provide concrete recommendations to guide the development of a coherent and comprehensive virus taxonomy.

Have a great Saturday!

Pregnancy and early life

The investigation of the association of pregnancy weight gain on maternal and neonatal gut microbiota composition and abundance using 16sRNA sequencing – Song and Liu – BMC Pregnancy and Childbirth

Human gut microbiome

The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population – Bourdeau-Julien et al. – Microbiome

Review: Conversations in the Gut: The Role of Quorum Sensing in Normobiosis – Markus et al. – International Journal of Molecular Sciences

Review: Gut Microbiome and Neurodevelopmental Disorders: A Link Yet to Be Disclosed – Illiodromiti et al. – Microorganisms

Natural Green Spaces, Sensitization to Allergens, and the Role of Gut Microbiota during Infancy – Buchholz et al. – mSystems

Animal experiments

Mimicking seasonal changes in light-dark cycle and ambient temperature modulates gut microbiome in mice under the same dietary regimen – Matsumoto et al – Plos One

Animal microbiome

Preprint: Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta – Moeller et al. – BioRxiV

Plant, root, and soil microbiome

Preprint: Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype – Simonin et al. – BioRxiV

Preprint: Viral but not bacterial community succession is characterized by extreme turnover shortly after rewetting dry soils – Santos-Medellin et al. – BioRxiV

Ecological drivers and potential functions of viral communities in flooded arsenic-contaminated paddy soils – Gao et al. – Science of the total environment

Water and extremophile microbiome

Preprint: Redefinition of archetypal phytoplankton-associated bacteria taxa based on globally distributed dinoflagellates and diatoms – Yang et al. – BioRxiV

Preprint: Plastic Leachate Exposure Drives Antibiotic Resistance and Virulence in Marine Bacterial Communities – Vlaanderen et al. – BioRxiV

Phages and viruses

Preprint: African army ants at the forefront of virome surveillance in a remote tropical forest – Fritz et al. – BioRxiV

Techniques

Preprint: Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction – Simon et al. – BioRxiV

Preprint: The long and short of it: Benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies – Cook et al. – BioRxiV

Non microbiology pick

Opinion: Four principles to establish a universal virus taxonomy – Simmonds et al. – PLoS Biology

February 4th, 2023

Posted on February 4, 2023 by Alise Ponsero

Bonjour from Paris, France !

In today’s digest you will find a wide variety of interesting preprints and published research papers encompassing very interesting microbiome such as Yak calves rumen, compost, wineyard soil and lichen symbionth microbiota!

If you are interested in virome, I recommend looking at the fascinating preprint from Ha and collaborators investigating the biogeography of giant viruses from the phylum Nucleocytoviricota. They leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to recovered novel genomes from these viruses and identified geographical patterns of distribution.

If you are working on human microbiomes, I recommend checking out a really interesting preprint, comparing the biases and strengths of four commercially available DNA extraction kits frequently used for whole genome shotgun analysis of the human microbiome.

Have a great Saturday!

Events and jobs

Event: Cell Symposia: Infection biology in the age of the microbiome. Paris, France June 7-9

Event: 55th Annual Meeting of the European Society for Paediatric Gastroenterology, Hepatology and Nutrition. Vienna, Austria 17-20 May

Pregnancy and early life

Insufficient Evidence of a Breastmilk Microbiota at Six-Weeks Postpartum: A Pilot Study – Leech et al. – Nutrients

Effects of Perinatal Antibiotic Exposure and Neonatal Gut Microbiota – Morreale et al. – Antibiotics

Necrotizing Enterocolitis: The Role of Hypoxia, Gut Microbiome, and Microbial Metabolites – Kaplina et al. – International Journal of Molecular sciences

Human gut microbiome

Preprint: Functional assignment of gut-specific archaeal proteins in the human gut microbiome – Novikova et al. – BioRxiv

Animal microbiome

Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea – Woo et al. – PLOS ONE

The association between gingivitis and oral spirochetes in young cats and dogs – Yamaki et al. – PLOS ONE

Maternal rumen and milk microbiota shapes the establishment of early-life rumen microbiota in grazing yak calves – Guo et al. – Journal of Dairy Science

Plant, root, and soil microbiome

Preprint: Fundamentals of biofilm formation in soil: From functionalized self-assembled monolayers to rewilding – Hendiani et al. – BioRxiv

Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards – Steiner et al. – PLOS ONE

Preprint: Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes – Tagirdzhanova et al. – BioRxiv

Water and extremophile microbiome

Preprint: Assessing the biogeography of marine giant viruses in four oceanic transects – Ha et al. – BioRxiv

Preprint: Cross-domain interactions induce community stability to benthic biofilms in proglacial streams – Busi et al. – BioRxiv

Opinion: Viral infection in the ocean—A journey across scales – Vincent and Vardi – PLOS biology

Bioinformatics

Preprint: Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome – Van Dijk et al – BioRxiv

Techniques

Preprint: Comparison of commercial DNA extraction kits for whole metagenome sequencing of human oral, vaginal, and rectal microbiome samples – Wright et al – BioRxiv

October 12th, 2021

Posted on October 12, 2021 by Alise Ponsero

Bonjour from Paris, France ! Today’s digest contains a selection of really interesting preprints and published studies. In their review, Heilbronner and collaborators explore the role of bacteriocins, small antibacterial molecules produced by many commensal bacteria in human-associated microbiomes. The role of the bacteriocins in the human microbiome is of particular importance since they could be leveraged to specifically target colonizing pathogens while sparing mutualistic patners.

If you are interested in exploring new bioinformatic methods, I recommend taking a look at the study from Cheng and collaborators, who applied a novel iterative random forest approach to explore marine microbiome during algal blooms. They show how this model allow to identify conditions that are important causal factors of algal bloom dynamics.

Today’s non-microbiology pick is an opinion piece reflecting on the possible methods to develop the field of computational biology, ensure proper training and career development in this discipline and allow a greater collaboration between domain biologist and data scientists in multidisciplinary teams.

Have a great Tuesday!

Events and jobs

Virtual conference: Harnessing the plant microbiome – October 22-24, 2021
University of California, Davis, USA

Virtual conference: Reshaping the Microbiome through nutrition – November 17-19, 2021

General microbiome

Review: The microbiome-shaping roles of bacteriocins – Heilbronner et al. – Nature Reviews Microbiology

Human gut microbiome

Preprint: Gut Bacterial Dysbiosis and Instability is Associated with the Onset of Complications and Mortality in COVID-19 – Schult et al. – BioRXiv

Review: Nurturing the Early Life Gut Microbiome and Immune Maturation for Long Term Health – Dogra et al. – microorganisms

Animal experiments

Preprint: Mice with a humanized immune system are resilient to transplantation of human microbiota – Zhou et al. – BioRXiv

Animal microbiome

Preprint: Inter-species microbiota transplantation recapitulates microbial acquisition and persistence in mosquitoes – Coon et al. – BioRXiv

Water and extremophile microbiome

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms – Cheng et al. – Scientific reports

Built environment

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years – Wang et al. – Microbiome

Phages and viruses

Preprint: A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use – Hegarty et al. – BioRXiv

Bioinformatics

Preprint: SynTracker: a synteny based tool for tracking microbial strains – Enav and Ley – BioRXiv

My non-microbiology pick

A field guide to cultivating computational biology – Way et al – PLOS biology

August 22nd, 2021

Posted on August 21, 2021 by Alise Ponsero

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of really interesting preprints and published studies. If you are interested in soil microbiology, take a look at the preprint by Nelson and collaborators, who characterized the soil microbiome across a wildfire burn severity gradients in coniferous forests and made their dataset available in the Fire Responding Ecogenomic database (FiRE-db).

Looking at a large variety of ecosystems, Rodriguez-Gijon and collaborators used a vast collection of Metagenomes Assembled Genomes (MAGs), to investigate the genomes size of prokaryotes in these ecosystems. They show that, while the environment of origin can be linked to genome size, it seems like evolutionary phylogenetic history is in many cases a stronger predictor.

Finally, today’s non-microbiology pick is a great “10 simples rules” paper reviewing best practices on organizing bioinformatics workshops in low and middle-income countries.

Have a great Weekend!

General microbiome

Preprint: A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy – Rodriguez-Gijon et al. – BioRXiV

Multi-site human microbiome

Review : Host-Microbe Metagenomics: a Lens To Refocus Our Perspective
on Infectious and Inflammatory Diseases – Kalantar and Langelier – mSystems

Human gut microbiome

Rectal bacteriome and virome signatures and clinical outcomes in community-acquired pneumonia: An exploratory study – Kullberg et al. – EClinicalMedicine

Review: The important role of fungi in inflammatory bowel diseases – Wang et al. – Scandinavian Journal of Gastroenterology

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

Preprint: A bacterial genome and culture collection of gut microbial in weanling piglet – Dong et al. – BioRXiV

Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms – Lührmann et al. – Plos One

Plant, root, and soil microbiome

Preprint: Does plant diversity determine the diversity of the rhizosphere microbial community? – Zverev et al. – BioRXiV

Preprint: Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire – Nelson et al. – BioRXiV

Peatland microbial community responses to plant functional group and drought are depth-dependent – Lamit et al. – Molecular ecology

Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China – Ni et al. – Global ecology and Biogeography

Water and extremophile microbiome

Preprint: The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments – Nishimura et al. – BioRXiV

Food microbiology

Preprint: Mixed culture metagenomics of the microbes making sour beer – Piraine et al. – BioRXiV

Preprint: Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh – Tanzina et al. – BioRXiV

Preprint: Microbial communities in retail draft beers and the biofilms they produce – Bose et al. – BioRXiV

Bioinformatics

Book chapter: Bioinformatics Tools and Software – Gupta et al. – Advances in Bioinformatics, Springer, Singapore

MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes – Lee et al. – New biotechnology

My non-microbiology picks

Ten simple rules for organizing a bioinformatics training course in low– and middle-income countries – Moore et al. – PLOS computational biology

July 2nd, 2021

Posted on July 2, 2021 by Alise Ponsero

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of interesting gut microbiome papers and preprints. In particular, Beller et al. looked at the succession of microbial communities in the infant gut from birth to 1 year of age. This digest also contains some very interesting works on environmental microbiome, as an example, Wasmund et al. investigated bacterial taxa able to degrade extracellular DNA in marine sediments.

For those interesting in bioinformatic tools and methods, this digest also contains the description of novel data ressources and tools. In particular, Pellow et al. present a new tool, SCAPP, allowing for a better assembly of plasmids from metagenomes.

Finally, today’s non-microbiology pick is a paper looking critically at the open source citation advantage effect (the hypothesis that articles made available open access may benefit from an increased number of citation) by conducting a meta-analysis of previous studies.

Have a great Weekend!

Multi-site human microbiome

Review: The human microbiome and COVID-19: A systematic review – Yamamoto et al. – Plos One

Human gut microbiome

The gut microbiome and type 2 diabetes status in the Multiethnic Cohort – Maskarinec et al. – Plos One

Preprint: Niche partitioning facilitates coexistence of closely related gut bacteria – Brochet et al. – BiorXiV

Preprint: Successional Stages in Infant Gut Microbiota Maturation – Beller et al. – BiorXiV

Fetal meconium does not have a detectable microbiota before birth – Kennedy et al. – Nature Microbiology

Animal experiments

Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study – Tal et al. – NPJ Biofilms and Microbiomes

Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance – Liu et al. – Nature Microbiology

Animal microbiome

Preprint: Enteric viruses nucleic acids distribution along the digestive tract of rhesus macaques with idiopathic chronic diarrhea – Delwart et al. – BiorXiV

Plant, root, and soil microbiome

Microbiomes of commercially-available pine nuts and sesame seeds – Fay et al. – Plos One

Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication – Van Cauwenberghe et al. – ISME Journal

Water and extremophile microbiome

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments – Wasmund et al. – Nature Microbiology

Phages and viruses

Preprint: High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems – Meaden et al. – BioRxiV

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome – Nayfach et al. – Nature Microbiology

Bioinformatics

SCAPP: an algorithm for improved plasmid assembly in metagenomes – Pellow et al. – Microbiome

A standardized archaeal taxonomy for the Genome Taxonomy Database – Rinke et al. – Nature Microbiology

My non-microbiology picks

Is the open access citation advantage real? A systematic review of the citation of open access and subscription-based articles – Langham-Putrow et al. – Plos One

June 6th, 2021

Posted on June 6, 2021 by Alise Ponsero

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a variety of interesting papers,in particular for people interested in viromes. The digest contains a really interesting preprint on the diversity of four new Antarctic sea ice bacteriophages, demonstrating their uniqueness and novelty compared to previoulsy characterized phages.

For people interested in bacterial microbiome, this digest contains a lot of very interesting pieces, in particular a very interesting review on the hopes and current limitation of Fecal Microbial Transplants in clinical settings.

Finally, today’s non-microbiology pick is a piece exploring the social impacts of naming diseases using strong-held but flawed names like German measles,

Have a great Weekend!

Human gut microbiome

Impact of the Gut Microbiota Balance on the Health–DiseaseRelationship: The Importance of Consuming Probioticsand Prebiotics – Olvera-Rosales et al. – Foods

Review: Fecal microbiota transplantationin human metabolic diseases:From a murky past to a bright future? – Hanssen et al. – Cell

Animal experiments

Short- and long-term effects of amoxicillin/clavulanic acid or doxycycline on the gastrointestinal microbiome of growing cats – Stavroulaki et al. – BioRxiv

Plant, root, and soil microbiome

Preprint: Deep-rooted plant species recruit distinct bacterial communities in 3 m deep subsoil – Bak et al. – BioRxiV

Preprint: Single seed microbiota: assembly and transmission from parent plant to seedling – Chesneau et al. – BioRxiV

Built environment

Reconstruction of metagenome-assembled genomes from aquaria – Ettinger et al. – BiorXiV

Phages and viruses

Viruses roam the wheat phyllosphere – Forero-Junco et al. – BioRxiV

Characteristics of genetically diverse Antarctic sea ice bacteriophages allow adaptation to changing environmental conditions – Demina et al. – BioRxiv

Bioinformatics

Preprint: PGfinder, a novel analysis pipeline for the consistent, reproducible and high-resolution structural analysis of bacterial peptidoglycans – Patel et al. – BioRxiV

Perspective: Computational Viromics: Applications of the Computational Biology in Viromics Studies – Lu and Peng – Virologica Sinica

Preprint: Detecting the hosts of bacteriophages using GCN-Based semi-supervised learning – Shang and Sun – ArxiV

My non-microbiology picks

Preprint: Naming of human diseases on the wrong side of history – Hu – BioRxiV

May 8th, 2021

Posted on May 8, 2021 by Alise Ponsero

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a variety of interesting papers, in particular in bioinformatics! I recommend anyone interesting in metagenomic read classification to take a look at the benchmark study by Arizmendi Cardenas and collaborators. They compared read-based taxonomic classification tools on their capacity to handle ancient DNA sequences, characterized by a higher mutation rate and shorter sequences.

This digest also contains a very good review on the current state of the art network analysis methods for exploring interaction in complex microbial communities.

Finally, today’s non-microbiology pick is a piece exploring the current challenges and limitations for the annotation of microbiome dataset with high-quality metadata.

Have a great Weekend!

Human gut microbiome

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease – Aldars-Garcia et al. – Microorganisms

Animal experiments

Millet-based supplement restored gut microbial diversity of acute malnourished pigs – Li et al. – PLOS One

A mixture of quebracho and chestnut tannins drives butyrate-producing bacteria populations shift in the gut microbiota of weaned piglets – Miragoli et al. – PLOS One

Animal microbiome

Dynamic changes occur in the DNA gut virome of female cynomolgus macaques during aging – Tan et al. – Microbiology Open

Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France – Nebbak et al. – Viruses

Plant, root, and soil microbiome

Preprint: Mapping the microbial diversity and natural resistome of north Antarctica soils – Marcoleta et al. – BioRXiv

Community dynamics in rhizosphere microorganisms at different development stages of wheat growing in confined isolation environments – Ma et al. – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Book chapter: Bioprospecting Extreme Ecosystems Before They Vanish: The (Poorly Studied) Microbiology of Tropical Glaciers – Yarzabal – Extreme environment (CRC press)

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores – Pearman et al. – PLOS One

Bioinformatics

Preprint: Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study – Arizmendi Cardenas et al. – BioRXiv

Review: Network analysis methods for studying microbial communities: A mini review – Matchado et al. – Computational and sctructural Biotechnology Journal

Improving metagenomic binning results with overlapped bins using assembly graphs – Mallawaarachchi et al. – Algorithms for molecular biology

My non-microbiology picks

Preprint: Current challenges in microbiome metadata collection – Rosenfeld et al. – BioRXiv

April 24th, 2021

Posted on April 24, 2021 by Alise Ponsero

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a wide range of topics to explore! I particularly recommend taking the time to read at the fascinating review listed below exploring horizontal gene transfer in environmental microbial communities. They describe how advances in the computational analysis of metagenomic data has allowed us to dive deeper in understanding these processes in microbiomes.

Among the list of very interesting research papers in this digest, you’ll find a fascinating study exploring the symbiotic microbial communities associated with deeper corals. Although extensive litterature has been published on coral microbiomes from shallow waters, this papers is the first to examine microbial communities associated with the deep photosymbiotic corals, living at more than 150 m of depth!

Today’s non-microbiology pick is a really interesting paper from Faldelmola and collaborators reporting on the development by the Pan-African H3Africa Bioinformatics Network of two data portals for African genomic medicine and African microbiomes datasets. The paper explore how they lead a very successful 6-days hackathon allowing to efficiently develop these two important scientific ressources, but also how they build a collaborative community of African researchers and experts.

Have a great Weekend!

General microbiome

Review: Examining horizontal gene transfer in microbial communities – Brito – Nature reviews microbiology

Preprint: Evidence for a billion-years arms race between viruses, virophages and eukaryotes – Barreat and Katzourakis – BioRxiV

Unifying community detection across scales from genomes to landscapes – Hudon et al. – Oikos

Human gut microbiome

Preprint: Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Watson et al. – BioRxiV

Animal experiments

Diversity and characteristics of raw milk microbiota from Korean dairy farms using metagenomic and culturomic analysis – Ryu et al. – Food control

Animal microbiome

Preprint: Reclassification of seven honey bee symbiont strains as Bombella apis – Smith et al. – BioRxiV

Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth) – Rouzé et al. – ISME Journal

Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes – Thongsripong et al. – Scientific reports

Water and extremophile microbiome

Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents – McAllister et al. – ISME Journal

Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones – Sun et al. – ISME Journal

Morphological complexity affects the diversity of marine microbiomes – Lemay et al. – ISME Journal

Preprint: Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic – Ferreira et al. – BioRxiV

Bioinformatics

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC – Parrello et al. – Plos One

A roadmap for metagenomic enzyme discovery – Robinson et al. – Natural Product Reports

Techniques

Preprint: Synergistic effect of short- and long-read sequencing on functional meta-omics – Galata et al. – BioRxiV

My non-microbiology picks

H3ABioNet genomic medicine and microbiome data portals hackathon proceedings – Fadlelmola et al. – Database

March 28th, 2021

Posted on March 28, 2021 by Alise Ponsero

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in marine microbiology and virology, I recommend taking a look at the paper by Gazitúa and collaborators. In this study they investigated the role of phages in shaping the metabolism metabolic networks along redox gradients associated with marine oxygen minimum zones. To do so, they investigated the phage contents in auxiliary metabolic genes involved in bacterial photosynthesis, central carbon metabolism, and nutrient cycling.

Today’s non-microbiology pick is a web-platform, called Sysrev, built to aid in systematic evidence reviews. Sysrev contains thousands of Findable, Accessible, Iteroperable and Reusable (FAIR) datasets from a large variety of disciplines.

Have a great Sunday!

Human gut microbiome

Preprint: Fecal microbiome of children with norovirus gastroenteritis – Merces Hernandez et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands – Wang et al. – bioRxiv

Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. – Bernard et al. – ISME J

Distribution patterns of Acidobacteriota in different fynbos soils – Conradie and Jacobs – PLOS

Water and extremophile microbiome

Preprint: Epidemiological dynamics of viral infection in a marine pico-eukaryote – Listmann et al. – bioRxiv

Preprint: A deep-sea sulfate reducing bacterium directs the formation of zero-valent sulfur via sulfide oxidation – Liu et al. – bioRxiv

Preprint: Integrated multi-omics investigations reveal the key role of synergistic microbial networks in removing plasticizer di-(2-ethylhexyl) phthalate from estuarine sediments – Ting-Shyang Wei et al. – bioRxiv

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community – Seyler et al. – ISME J