Category Archives: Animal microbiome

May 12, 2023

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Today’s digest features studies on human respiratory tract, mouse models, bovine milk microbiome, and more. See you at #MVIF next week!

Respiratory tract microbiome

Review: Ecology of the respiratory tract microbiome – Ana Elena Pérez-Cobas – Trends in Microbiology

Cervicovaginal microbiome

The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by Lactobacillus iners regardless of HPV status – Daniela Vargas-Robles – bioRxiv

Gut microbiome

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic – Serena Porcari – Cell Host & Microbes

Profiling the human intestinal environment under physiological conditions – Dari Shalon – Nature

Interaction between gut microbiota and sex hormones and their relation to sexual dimorphism in metabolic diseases – Jose Antonio Santos-Marcos – Biology of Sex Differences

Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis – Paige Salerno – bioRxiv

Animal microbiome

Metagenomic analysis of milk microbiota in the bovine subclinical mastitis – Giulia Alessandri – bioRxiv

Animal experiments

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice – Paolo Manghi – Cell Reports

Bioinformatics

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning – Olga Mineeva – Plos Computational Biology

Technique

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing – David Calderón-Franco – Antonie van Leeuwenhoek

Built environment

The microbiome of an outpatient rehabilitation clinic and predictors of contamination: A pilot study – Gabriella Brigando – PlosOne

May 5, 2023

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Today’s microbiome digest is a grab bag that includes ten simple rules for working with other people’s code, an article examining Wolbachia infections in native cockroach populations, and an article examining the role in lactic acid in shaping the human microbiome. Also highlighted is an article focused on human viruses residing within our cells and tissues, which demonstrated a unique virome in nine different human organs through targeted-enrichment viral metagenomics and virus specific qPCRs.

Happy reading!

General microbiome

The structure of prevacuolar compartments in Neurospora crassa as observed with super-resolution microscopy – Bowman – PLOS One

Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences – Nakano et al. – PLOS One

***Unmasking the tissue-resident eukaryotic DNA virome in humans – Pyöriä et al. – Nucleic Acids Research

Predicting partner fitness based on spatial structuring in a light-driven microbial community – Sakkos et al. – PLOS Computational Biology

Multi-site human microbiome

Evaluation of alcohol-free mouthwash for studies of the oral microbiome – Yano et al. – PLOS One

A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome – Zhang et al. – Microbiome

Human gut microbiome

Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment – Hao et al. – Microbiome

Animal microbiome

Wolbachia infection in native populations of Blattella germanica and Periplaneta americana – Choubdar et al. – PLOS One

Plant, root, and soil microbiome

Bacterial and fungal community composition and community-level physiological profiles in forest soils – Kunito et al. – PLOS One

Water and extremophile microbiome

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks – Liu et al. – Microbiome

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes – Muñoz-Marín et al. – PLOS One

Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages – Tong et al. – Microbiome

Bioinformatics

Ten simple rules for working with other people’s code – Pilgrim et al. – PLOS Computational Biology

Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier – Raza et al. – PLOS One

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria – Roux et al. – PLOS Biology

April 26, 2023

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General microbiome

[PREPRINT]Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Klümper et al. – bioRxiv

Pregnancy and early life

First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes – Graspeuntner et al. – Microbiology Spectrum

Human gut microbiome

Mucin-microbiome signatures shape the tumor microenvironment in gastric cancer – Oosterlinck et al. – Microbiome

[REVIEW]Fecal microbiota transplantation for recurrent C. difficile infection in patients with inflammatory bowel disease: A systematic review and meta-analysis – Porcari et al. – Journal of Autoimmunity

[REVIEW]Alcohol, the gut microbiome, and liver disease – Jew & Hsu – JGH

[REVIEW]Microbial metabolites in colorectal tumorigenesis and cancer therapy – Liu et al. – Gut Microbes

Human biliary microbiome

Neoadjuvant therapy does not impact the biliary microbiome in patients with pancreatic cancer – Behrens et al. – Journal of Surgical Oncology

Animal microbiome (for animals in the wild)

Indirect maternal effects via nest microbiome composition drive gut colonization in altricial chicks – Diez-Mendez et al. – Molecular Ecology

The gut microbiome of solitary bees is mainly affected by pathogen assemblage and partially by land use – de Landa et al. – Environmental Microbiome

Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin – Masasa et al. – Microbiology Spectrum

The microbiota in feces of domestic pigeons in Seoul, Korea – Oh et al. – Heliyon

Plant, root, and soil microbiome

Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau – Solis Pino et al. – BMC Plant Biology

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

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem – Cackovic et al. – mSphere

Bioinformatics

[PREPRINT]ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization – Yang et al. – arXiv

April 19, 2023

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Pregnancy and early life

[REVIEW]The maternal gut microbiome during pregnancy and its role in maternal and infant health – Sinha et al. – Current Opinion in Microbiology

Human oral microbiome

Independent Effects of HIV and Antiretroviral Therapy on the Oral Microbiome Identified by Multivariate Analyses – Beall et al. – mBio

[REVIEW]Oral microbial changes and oral disease management before and after the treatment of hematological malignancies: a narrative review – Lin et al. – Clinical Oral Investigations

Human vaginal microbiome

[REVIEW]Gardnerella Revisited: Species Heterogeneity, Virulence Factors, Mucosal Immune Responses, and Contributions to Bacterial Vaginosis – Shvartsman et al. – Infection and Immunity

Human gut microbiome/virome

[REVIEW]Intrahost evolution of the gut microbiota – Barreta & Gordo – Nature Reviews Microbiology

The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice – Fan et al. – Nature Microbiology

Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori – Wang et al. – Nature Communications

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Spatz et al. – Microbiome

Metabolic independence drives gut microbial colonization and resilience in health and disease – Watson et al. – Microbiome

Development of the gut microbiota in the first 14 years of life and its relations to internalizing and externalizing difficulties and social anxiety during puberty – Ou et al. – European Child & Adolescent Psychiatry

Reconstructing the landscape of gut microbial species across 29,000 diverse individuals – Segota et al. – NAR

Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease – Poudel et al. – PLOS One

Seasonal variations in gut microbiota and disease course in patients with inflammatory bowel disease – Tani et al. – PLOS One

The convergent application of metabolites from Avena sativa and gut microbiota to ameliorate non-alcoholic fatty liver disease: a network pharmacology study – Oh et al. – Journal of Translational Medicine volume

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

Effects of Extended Cage Component Sanitation Interval on the Microenvironment, Health, and Gastrointestinal Microbiome of Rats (Rattus norvegicus) – Taylor et al. – Journal of the American Association for Laboratory Animal Science

Music-based interventions in the feeding environment on the gut microbiota of mice – Niu et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality – Maidment et al. – Microbiome

[PREPRINT]Microbiome variability of mosquito lines is consistent over time and across environments – Accoti et al. – bioRxiv

Differences in the luminal and mucosal gut microbiomes and metabolomes of oriental rat snake (Ptyas mucosus) – Wei et al. – Applied Microbiology and Biotechnology

Bioinformatics

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Bazant et al. – Microbiome

Techniques

Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle – Liu et al. – Microbiome

March 22, 2023

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Human gut microbiome

NEMoE: a nutrition aware regularized mixture of experts model to identify heterogeneous diet-microbiome-host health interactions – Xu et al. – Microbiome

The gut microbiome in social anxiety disorder: evidence of altered composition and function – Butler et al. – Translational Psychiatry

Analysis of the fecal metagenome in long-term survivors of pancreas cancer – Kharofa et al. – Cancer

Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention – Watanabe et al. – Nature Medicine

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

New insights into the impact of microbiome on horizontal and vertical transmission of a tick-borne pathogen – Du et al. – Microbiome

Periodontitis exacerbates atherosclerosis through Fusobacterium nucleatum-promoted hepatic glycolysis and lipogenesis – Zhou et al. – Cardiovascular Research

Gut microbiota in a mouse model of obesity and peripheral neuropathy associated with plasma and nerve lipidomics and nerve transcriptomics – Guo et al. – Microbiome

Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy – Vernaci et al. – The Oncologist

Plant, root, and soil microbiome

Environments and host genetics influence the geographic distribution of plant microbiome structure – Wei & Tan – bioRxiv

Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women – Ke et al. – Psychological Medicine

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

Core species and interactions prominent in fish-associated microbiome dynamics – Yamjima et al. – Microbiome

March 20, 2023

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Human and General Microbiome

Bacteria require phase separation for fitness in the mammalian gut – Emilia Krypotou – Science

Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets – Jonathan J Panzer – BMC Microbiology

Gut-microbiome-expressed 3β-hydroxysteroid dehydrogenase degrades estradiol and is linked to depression in premenopausal females – Di Li – Cell Metabolism

Metagenomic association analysis of cognitive impairment in community-dwelling older adults – Jincheng Li – Neurobiology of Disease

Fusobacterium nucleatum promotes esophageal cancer early occurrence through upregulation of IL-32/PRTN3 expression – Jing Lei – Cancer Science

Review: Postbiotics Implication in the Microbiota-Host Intestinal Epithelial Cells Mutualism – Harpreet Kaur – Probiotics and Antimicrobial Proteins

Review: Microbiota and growth among infants and children in low-income and middle-income settings – James M Njunge – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective – Mireia Valles-Colomer – Nature Medicine

Review: Oral polymicrobial communities: Assembly, function, and impact on diseases – George Hajishengallis – Cell Host & Microbe

Review: Gut microbiota: a non-target victim of pesticide-induced toxicity – Tusha Sharma – Gut Microbes

Perspective: Human microbiome research: Growing pains and future promises – Jens Puschhof – PLoS Biology

Beneficial Microbes and Compounds

Versatility of bacterial outer membrane vesicles in regulating intestinal homeostasis – Xinyue Wang – Science Advances

Lactobacillus rhamnosus GG cell-free supernatant as a novel anti-cancer adjuvant – Rossella Salemi – Journal of Translational Medicine

Environmental Microbiome

Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy – Eke I Kalu – ISME Communications

Other Microbes

Biointerface mineralization generates ultraresistant gut microbes as oral biotherapeutics – Zhongmin Geng – Science Advances

Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli – Tracy H Hazen – Nature Communications

Microbiome Analysis: Tools and Techniques

Spatial profiling of microbial communities by sequential FISH with error-robust encoding – Zhaohui Cao – Nature Communications

sBGC-hm: An atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome – Huixi Zou – Bioinformatics

Protocol: Bioinformatic and Statistical Analysis of Microbiome Data – Youngchul Kim – Methods in Molecular Biology

Protocol: Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications – Xuefeng Wang – Methods in Molecular Biology

March 8, 2023

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Pregnancy and early life

[PREPRINT]The influence of early life exposures on the infant gut virome – Zhang et al. – bioRxiv

[PREPRINT]Maternal diet and gut microbiome composition modulate early life immune responses – Grant et al. – bioRxiv

Human oral microbiome

Smoking-induced subgingival dysbiosis precedes clinical signs of periodontal disease – Tamashiro et al. – Scientific Reports

Human gut microbiome

Gut microbiota and risk of five common cancers: A univariable and multivariable Mendelian randomization study – Wei et al. – Cancer Medicine

The role of the sex hormone-gut microbiome axis in tumor immunotherapy – Wang et al. – Gut Microbes

[REVIEW]The Influence of the Microbiome on Aggressive Behavior: an Insight into Age Related Aggression – Gulledge, Oyebode & Donaldson – FEMS Microbiology Letters

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

Gnotobiotic mice housing conditions critically influence the phenotype associated with transfer of faecal microbiota in a context of obesity – Daoust et al. – Gut

Animal microbiome (for animals in the wild)

[REVIEW]The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions – Mohamed et al. – FEMS Microbiology Reviews

Comparison of the gut microbiome and resistome in captive African and Asian elephants on the same diet – Feng et al. – Front. Vet. Sci.

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

Core and conditionally rare taxa as indicators of agricultural drainage ditch and stream health and function – Shi et al. – BMC Microbiology

Species invasions shift microbial phenology in a two-decade freshwater time series – Rohwer et al. – PNAS

Bioinformatics

Controlling taxa abundance improves metatranscriptomics differential analysis – Ji & Ma – BMC Microbiology

coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies – Luz Calle, Pujolassos & Susin – BMC Bioinformatics

[PREPRINT]You can move, but you can’t hide: identification of mobile genetic elements with geNomad – Camargo et al. – bioRxiv

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing – Wick, Judd & Holt – PLOS Computational Biology

February 25th, 2023

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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

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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 13, 2023

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Today’s reading recommendation is a microbiota review collection edited by Lindsay Hall and Melanie Schirmer.

Happy Monday and see you at #MVIF!

Vaginal microbiome

Gardnerella Diversity and Ecology in Pregnancy and Preterm Birth – Hanna L. Berman – bioRxiv

Heterogeneity of the group B streptococcal type VII secretion system and influence on colonization of the female genital tract – Brady L. Spencer – bioRxiv

Urinary microbiome

Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains – Ananya Prasad – mSphere

Human gut

Gut microbes predominantly act as symbiotic partners rather than raw nutrients – Nuno Felipe da Silva Soares – bioRxiv

Antibiotic resistance in the commensal human gut microbiota – Lisa E Lamberte, Willem van Schaik – Current Opinion in Microbiology

Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting – Lharbi Dridi – Nature Communications

Animal experiments

Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice – Andrew J. Forgie – Microbiome

Disturbance of lipid metabolism in germ-free mice transplanted with gut microbiota of DSS-induced colitis mice – Chungho Lee – Plos One

Bioinformatics

Accurate and fast graph-based pangenome annotation and clustering with ggCaller – Samuel T. Horsfield – bioRxiv

Brief report: uBin – a manual refining tool for genomes from metagenomes – Till L V Bornemann – Environmental Microbiology

In-situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day – Javier Tamames – bioRxiv

The virtual microbiome: A computational framework to evaluate microbiome analyses – Belén Serrano-Antón – Plos One