Category Archives: Human respiratory

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

February 24, 2023

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Human and General Microbiome

Review: Gut microbiome lipid metabolism and its impact on host physiology – Brown et al. Cell Host & Microbe

Review: Modelling human immune responses using microbial exposures in rodents – Li and Baldridge. Nature Microbiology

Gut commensal Parabacteroides distasonis alleviates inflammatory arthritis – Sun et al. Gut

An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson’s disease participants – Hall et al. Nature Communications

Antibiotic use and inflammatory bowel disease: number needed to harm? – Ludvigsson. Gut

Oral & Respiratory Microbiome

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis – Brewer et al. Science Translational Medicine

Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease – Abotsi et al. Microbiome

Animal experiments

Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut – Zhang et al. Nature Microbiology

Microbe-mediated intestinal NOD2 stimulation improves linear growth of undernourished infant mice – Schwarzer et al. Science

Gamma-delta T cells modulate the microbiota and fecal micro-RNAs to maintain mucosal tolerance – Rezende et al. Microbiome

Phages and viruses

Review: Bacteriophage discovery to advance biotechnology and biotherapeutics – Mu and Lawley Nature Reviews Microbiology

Bioinformatics

Impact of microbial genome completeness on metagenomic functional inference – Eisenhofer et al. ISME

Pharokka: a fast scalable bacteriophage annotation tool – Bouras et al. Bioinformatics

Non Microbiome Picks

A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA and adenovirus vectored vaccines – Ryan et al. Cell Reports Medicine

Influenza-trained mucosal-resident alveolar macrophages confer long-term antitumor immunity in the lungs – Wang et al. Nature Immunology

November 30, 2022

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Human respiratory microbiome

Airway microecology in rifampicin-resistant and rifampicin-sensitive pulmonary tuberculosis patients – Cai et al. – BMC Microbiology

Human oral microbiome

Oral Bacteriome and Mycobiome across Stages of Oral Carcinogenesis – Heng et al. – Microbiology Spectrum

Human gut microbiome

[REVIEW]Double-edged sword: impact of fecal microbiome transplants on the gut resistome – Hallowell, Gao & Suez – Current Opinion in Gastroenterology

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation – Federici et al. – Cell

Gut microbiome alterations in preclinical Alzheimer’s disease – Jung et al. – PLOS One

[REVIEW]Sex, puberty, and the gut microbiome – Sisk-Hackworth, Kelley & Thackray

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

Lactobacillus reuteri tryptophan metabolism promotes host susceptibility to CNS autoimmunity – Montgomery et al. – Microbiome

Animal microbiome (for animals in the wild)

Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont – Sylvain et al. – Microbiology Spectrum

Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids – Haji et al. – Scientific Reports

Plant, root, and soil microbiome

Unveiling the Wheat Microbiome under Varied Agricultural Field Conditions – Jaiswal et al. – Microbiology Spectrum

Changes of the microbial community in kiwifruit during storage after postharvest application of Wickerhamomyces anomalus – Zhao et al. – Food Chemistry

Food microbiology

[PREPRINT]A dark matter in sake brewing: Origin of microbes producing a Kimoto-style fermentation starter – Ito et al. – bioRxiv

November 14, 2022

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Human and General Microbiome

Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits – Lili Liu – Nature Communications

Kidney microbiota dysbiosis contributes to the development of hypertension – Xin-Yu Liu – Gut Microbes

Gut mycobiota dysbiosis in drug-naïve, first-episode schizophrenia – Xiuxia Yuan – Schizophrenia Research

Transcriptomic analysis reveals an association of FCGBP with Parkinson’s disease – Pilar Gómez-Garre – NPJ Parkinson’s Disease

Integration of stool microbiota, proteome and amino acid profiles to discriminate patients with adenomas and colorectal cancer – Sofie Bosch – Gut Microbes

Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites – Claudia Marcela Arenas-Gómez – Critical Reviews in Microbiology

Colibactin possessing E. coli isolates in association with colorectal cancer and their genetic diversity among Pakistani population – Habiba Tariq – PloS one

Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration – Yifan Zhou – The Journal of Experimental Medicine

Genome-microbiome interplay provides insight into the determinants of the human blood metabolome – Christian Diener – Nature Metabolism

Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study – Edgar Gulavi – BMC Microbiology

Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis – Zhixia Zhang – BMC Oral Health

Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome – Qin Liu – Nature Communications

Characterization of antibiotic-resistance traits in Akkermansia muciniphila strains of human origin – Rossella Filardi – Scientific Reports

Food Microbiome

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses – Ryosuke Unno – Microbiology Spectrum

Animal Microbiome

Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast – Gustavo Vasconcelos Bastos Paulino – Environmental Science and Pollution Research International

Environmental Microbiome

Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches – Beatrice Farda – Scientific Reports

Plant Microbiome

High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling – Kie Kumaishi – Scientific Reports

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure – Ana Paula Corrêa Moneda – Scientific Reports

Effects of Two Bacillus velezensis Microbial Inoculants on the Growth and Rhizosphere Soil Environment of Prunus davidiana – Huimin Shi – International Journal of Molecular Sciences

Review: Climate change and plant pathogens – Muhammad M Raza – Current Opinion in Microbiology

Bioinformatics and Microbiome Analysis

Faecal microbiome-based machine learning for multi-class disease diagnosis – Qi Su – Nature Communications

Wochenende – modular and flexible alignment-based shotgun metagenome analysis – Ilona Rosenboom – BMC Genomics

De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee – Yunxi Liu – Nature Communications

November 09, 2022

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General microbiome

[REVIEW]
Compartmentalization of the host microbiome: how tumor microbiota shapes checkpoint immunotherapy outcome and offers therapeutic prospects – Boesch et al. – Journal for ImmunoTherapy of Cancer

Human respiratory microbiome

The Upper-Airway Microbiome as a Biomarker of Asthma Exacerbations despite Inhaled Corticosteroid Treatment – Perez-Garcia – Journal of Allergy and Clinical Immunology

Human gut microbiome

Manipulating the microbiome to enhance oral tolerance in food allergy – Gonzalez-Visiedo – Cellular Immunology

Longitudinal transkingdom gut microbial approach towards decompensation in outpatients with cirrhosis – Bajaj et al. – Hepatology

Happy ageing by trusting our gut microbes – Jayaraman & Pettersson – Biochemical and Biophysical Research Communications

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

Curcumin improves insulin sensitivity in high-fat diet-fed mice through gut microbiota – Zhong et al. – Nutrition & Metabolism

Short-Term Tomato Consumption Alters the Pig Gut Microbiome toward a More Favorable Profile – Goggans et al. – Microbiology Spectrum

[PREPRINT]Lifelong temporal dynamics of the gut microbiome associated with longevity in mice – Takayasu et al. – bioRxiv

[PREPRINT]The gut microbiome has sexually dimorphic effects on bone tissue energy metabolism and multiscale bone quality in C57BL/6J mice – Vahidi et al. – bioRxiv

Animal microbiome (for animals in the wild)

Food provisioning results in functional, but not compositional, convergence of the gut microbiomes of two wild Rhinopithecus species: Evidence of functional redundancy in the gut microbiome – Li et al. – Science of The Total Environment

Phages and viruses

Expansion of the global RNA virome reveals diverse clades of bacteriophages – Neri et al. – Cell

Bioinformatics

C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data – Song & Zhou – BMC Bioinformatics

October 26, 2022

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General microbiome

[BOOK]Human Microbiome in Health and Disease – Part B – Progress in Molecular Biology and Translational Science

Pregnancy and early life

Relationships of the very low birth weight infant microbiome with neurodevelopment at 2 and 4 years of age – Sarkar et al. – Developmental Psychobiology

Human respiratory microbiome

The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis – Knudsen et al. – Microbiome

Human gut microbiome

Profiling the fungal microbiome after FMT for graft-versus-host disease: insights from a phase 1 interventional study – van Lier et al. – Transplantation and Cellular Therapy

Colorectal cancer, Vitamin D and microbiota: A double-blind Phase II randomized trial (ColoViD) in colorectal cancer patients – Bellerba et al. – Neoplasia

Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome – Piancone et al. – Scientific Reports

Animal microbiome

[DATA]Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages – Feng et al. – Scientific data

Tick transmission of Borrelia burgdorferi to the murine host is not influenced by environmentally acquired midgut microbiota – Narasimhan et al. – Microbiome

Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis – Bianchimano et al. – Microbiome

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds – Navine et al. – Molecular Ecology

Impact of Germinated Brown Rice and Brown Rice on Metabolism, Inflammation, and Gut Microbiome in High Fat Diet-Induced Insulin Resistant Mice – Zhao et al. – J. Agric. Food Chem.

Dietary Lactobacillus reuteri prevent from inflammation mediated apoptosis of liver via improving intestinal microbiota and bile acid metabolism – Lin et al. – Food Chemistry

Plant, root, and soil microbiome

Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin – Wen et al. – Microbiome

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction – Tom et al. – Microbiome

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

Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary – Guo et al. – Science of The Total Environment

Bioinformatics

LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis – Özkurt et al. – Microbiome

Techniques

[PREPRINT]Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes – McCully et al. – bioRxiv

A novel metagenome-derived viral RNA polymerase and its application in a cell-free expression system for metagenome screening – Han et al. – Scientif Reports

October 05, 2022

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Pregnancy and early life

Multi-omic factors associated with future wheezing in infants – Beheshti et al. – Pediatric Research

Multi-site human microbiome

Race is a key determinant of the human intratumor microbiome – Lua et al. – Cancer Cell

Human respiratory microbiome

Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance – Merenstein, Bushman & Collman – Microbiome

Human milk microbiome

Maternal weight status and the composition of the human milk microbiome: A scoping review – Daiy et al. – PLOS One

Human oral microbiome

Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study – Carda-Dieguez, Mazzez & Mira – Microbiome

Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection – Austin et al. – Communications Biology

Human gut microbiome

[REVIEW]SARS-CoV-2-associated gut microbiome alteration; A new contributor to colorectal cancer pathogenesis – Mozaffari et al. – Pathology – Research and Practice

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin – Ma et al. – Genome Biology

Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome – Kawano et al. – Cell

Rural environment reduces allergic inflammation by modulating the gut microbiota – Yang et al. – Gut Microbes

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

Six types of tea extracts attenuated high-fat diet-induced metabolic syndrome via modulating gut microbiota in rats – Zhou et al. – Food Research International

Adaptation of the gut holobiont to malnutrition during mouse pregnancy depends on the type of nutritional adversity – Connor et al. – The Journal of Nutritional Biochemistry

Animal microbiome (for animals in the wild)

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle – Teseo et al. – Microbiome

Comparative multiomics study of the effects of Ellagic acid on the gut environment in young and adult mice – Duan et al. – Food Research International

[REVIEW]Crosstalk between the microbiota and insect postembryonic development – Girard et al. – Trends in Microbiology

Culturomic, metagenomic, and transcriptomic-based characterization of commensal lactic acid bacteria isolated from domestic dogs using Caenorhabditis elegans as a model for aging – Kang et al. – Journal of Animal Science

Plant, root, sponge and soil microbiome

Recruitment of specific microbes through exudates affects cadmium activation and accumulation in Brassica napus – Wu et al. – Journal of Hazardous Materials

Novel trends of genome evolution in highly complex tropical sponge microbiomes – Kelly et al. – Microbiome

[Petroleum pollution affects soil chemistry and reshapes the diversity and networks of microbial communities](Ecotoxicology and Environmental Safety) – Li et al. –

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

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics – Seong et al. – Microbiome

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China – Chen et al. – Water Research

Bioinformatics/Software

Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics – Weissman et al. – mSystems

[SOFTWARE]PhyloDM is a high-performance library that converts a phylogenetic tree into a pairwise distance matrix. – Aaron Mussig – github

September 21, 2022

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Human respiratory microbiome

The Microbiota of Human Lung of Pulmonary Tuberculosis and the Alteration Caused by Anti-tuberculosis Drugs – Zhang et al. – Current Microbiology

Human urinary microbiome

Mechanisms of the intestinal and urinary microbiome in kidney stone disease – Miller et al. – Nature Reviews Urology

Human oral microbiome

Comparison of tumor-associated and nontumor-associated esophageal mucosa microbiota in patients with esophageal squamous cell carcinoma – Zhang et al. – Medicine

Human gut microbiome

Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients – Thompson et al. – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Early fecal microbiome transfer after donor defecation determines response in patients with moderate to severe ulcerative colitis – Singh et al. – Indian Journal of Gastroenterology

[REVIEW]Modulatory role of gut microbiota in cholesterol and glucose metabolism: Potential implications for atherosclerotic cardiovascular disease Atherosclerosis – Roessler et al. – Atherosclerosis

Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population – Bai et al. – Microbiome

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

Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle – Hoces et al. – PLOS Biology

Inhibitory effects of antibiotic-induced gut microbiota depletion on acute itch behavior in mice – Zhang et al. – Brain Research Bulletin

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Yang et al. – Microbiome

Animal microbiome (for animals in the wild)

Community and shotgun metagenomic analysis of Alligator mississippiensis oral cavity and GI tracts reveal complex ecosystems and potential reservoirs of antibiotic resistance – Perez-Marron et al. – Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology

Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia – Brinker et al. – Molecular Ecology

Plant, root, and soil microbiome

Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds – Loiola et al. – Science of The Total Environment

[REVIEW]Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture – Diwan, Rashid & Vaishnav – Microbiological Research

Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability – Phour & Sindhu – Planta

[OPINION]Plant microbiota dysbiosis and the Anna Karenina Principle – Arnault, Money & Vandenkoornhuyse

Food microbiology

Anthocyanin Addition to Kefir: Metagenomic Analysis of Microbial Community Structure – Aydin et al. – Current Microbiology

Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance – Calabrese et al. – Microbiome

September 14, 2022

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General microbiome

[PREPRINT]Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity – Puente-Sánchez et al. – bioRiv

Human airway microbiome

[PREPRINT]Genomic and ecologic characteristics of the airway microbial-mucosal complex – Cuthbertson et al. – bioRxiv

Animal microbiome (for animals in the wild)

[DATA ]A global dataset of microbial community in ticks from metagenome study – Liu et al. – Scientific Data

Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota – Liu et al. – Applied Microbiology and Biotechnology

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

[PREPRINT][Microbial community dynamics during a harmful Chrysochromulina leadbeateri bloom in northern Norway](Microbial community dynamics during a harmful Chrysochromulina leadbeateri bloom in northern Norway) – Aalto et al. – bioRxiv

August 24, 2022

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General microbiome

[REVIEW]Detecting bacterial adaptation within individual microbiomes – Liebermann – Phil. Trans. R. Soc. B

[REVIEW]Soil microbiomes and one health – Banerjee & van der Heijden – Nature Reviews Microbiology

Pregnancy and early life

Microbial Analysis of Umbilical Cord Blood Reveals Novel Pathogens Associated with Stillbirth and Early Preterm Birth – Vander Haar et al. – mBio

Human respiratory microbiome

The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis – Avalos-Fernandez et al. – Respiratory Research

Human saliva microbiome

Saliva microbiome, dietary, and genetic markers are associated with suicidal ideation in university students – Ahrens et al. – Scientific Reports

Human gut microbiome

The gut microbiota is associated with immune cell dynamics in humans – Schluter et al. – Nature

The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces – Vujkovic-Cvijin et al. – Science Translational Medicine

Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling – Kim et al. – ISME Communications

Correlation of inflammatory biomarkers with the diversity of Bacteroidaceae, Bifidobacteriaceae, Prevotellaceae and Lactobacillaceae families in the intestinal microbiota of patients with end stage renal disease – Asgharian et al. – Advances in Medical Sciences

Impact of the Host Microbiome on Vaccine Responsiveness: Lessons Learned and Future Perspective – Stefanetti & Kasper – Biochemistry

Location-specific signatures of Crohn’s disease at a multi-omics scale – Gonzalez et al. – Microbiome

Association of food insecurity on gut microbiome and metabolome profiles in a diverse college-based sample – Mohr et al. – Scientific Reports

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

The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes – Miranda et al. – mSystems

Microbes in space

Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome – Madrigal et al. – Microbiome

Bioinformatics

[PREPRINT]Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4 – Blanco-Miguez et al. – bioRxiv

Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data – Lin, Eggesbø & Peddada – Nature Communications

Techniques

Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing – Wiemann et al. – Gut Microbes

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples – Baker et al. – mSystems