Category Archives: Human oral

May 29, 2024

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Human microbiomes

Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction – Alex E. Mohr – Nature Communications

[PREPRINT] Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome – Abishek Goel – bioRxiv

Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome – Francesca De Fillipis – Nature Communications

The interrelation between microbial immunoglobulin coating, vaginal microbiota, ethnicity, and preterm birth – H.J. Schuster – BMC Microbiome

Porphyromonas gingivalis, a bridge between oral health and immune evasion in gastric cancer – Matías Muñoz-Medel – Frontiers in Oncology

Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study – Jung Soo Park – Journal of Periodontal Resaerch

Animal microbiome

Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis – S. Casaro – BMC Animal Microbiome

Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes – Shichun He – BMC Microbiology

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis – Yujie Meng – BMC Microbiome

Co-habiting ants and silverfish display a converging feeding ecology – Thomas Parmentier – BMC Biology

Temperature-dependent differences in mouse gut motility are mediated by stress – Alvin Han – Nature Lab Animal

Food microbiome

Evaluation of microbiota-induced changes in biochemical, sensory properties and volatile profile of kombucha produced by reformed microbial community – Hilal Kilmanoglu – Food Chemistry X

Plant, soil, and root microbiome

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle – Bridget B. McGivern – Nature Microbiology

[PREPRINT] Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils – Samuel E. Barnett & Ashley Shade – bioRxiv

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome – Yoko Masuda – BMC Microbiome

Water & extremophile microbiome

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution – Brune Jounnard & Concepcion Sanchez-Cid – BMC Microbiome

Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron – Biao Yu – Frontiers in Microbiology

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria – Subhash Yadav – BMC Microbiome

May 17, 2024

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Today’s digest features bioinformatics binning methods, healthy dogs, lakes in South Africa, and more. For the human gut microbiome studies, check out the latest digest (May 15, 2024) by Grace Deitzler.

See you at #MVIF!

Skin microbiome

Intraspecies warfare restricts strain coexistence in human skin microbiomes – Christopher P. Mancuso – bioRxiv

Oral microbiome

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study – Memduh Bingöl – Journal of Clinical Periodontology

Urinary microbiome

Microbroth dilution method for antibiotic susceptibility testing of fastidious and anaerobic bacteria of the urinary microbiome – Wilson Geaman – Microbiology Spectrum

Respiratory tract

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease – Nick Quinn-Bohmann – BMC Biology

Food microbiome

Microbial community structure of plant-based meat alternatives – Franz-Ferdinand Rochn – pj Science of Food

Plan, root, soil

Functional team selection: a framework for local adaptation in plants and their belowground microbiomes – Nancy Collins Johnson and César Marín – ecoevoRxiv

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert – Patricio Arros – bioRxiv

Animal microbiome

Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial – Silke Salavati Schmitz – Access Microbiology

Early-life factors shaping the gut microbiota of Common buzzard nestlings – Hugo Pereira – Animal Microbiome

Animal experiment

13C-Stable isotope resolved metabolomics uncovers dynamic biochemical landscape of gut microbiome-host organ communications in mice – Xia Xiao – Microbiome

Water microbiome

Metagenomics datasets of water and sediments from eutrophication-impacted artificial lakes in South Africa – Grace Nkechinyere Ijoma – Scientific Data

Bioinformatics

Fairy: fast approximate coverage for multi-sample metagenomic binning – Jim Shaw and Yun William Yu – bioRxiv

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods – Daniel M Portik – biorXiv

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level – Amy S Graham – bioRxiv

Full factorial construction of synthetic microbial communities – Juan Diaz-Colunga – bioRxiv

ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences – Yao Pei – Microbiome

April 12, 2024

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Today’s digest features human gut microbiome studies on dietary fiber and fasting glucose, ocean microbiome, pangenome approaches, and more.

See you at #MVIF!

Oral microbiome

Saliva sampling method influences oral microbiome composition and taxa distribution associated with oral diseases – Cristian Roca – PlosOne

Gut microbiome

Changes in the intestinal microbiota of individuals with non-alcoholic fatty liver disease based on sequencing: An updated systematic review and meta-analysis – Wenpin Cai – PlosOne

Gut microbiota differences in stunted and normal-lenght children aged 36–45 months in East Nusa Tenggara, Indonesia – Ingrid S. Surono – PlosOne

Integrating research on bacterial pathogens and commensals to fight infections—an ecological perspective – Lisa Maier – The Lancet Microbe

Recommendations for the Use of Dietary Fiber to Improve Blood Pressure Control – Hamdi A. Jama – Hypertension

Review: Prebiotic selection influencing inflammatory bowel disease treatment outcomes: a review of the preclinical and clinical evidence – Amin Ariaee – eGastroenterology

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments – Torben Soelbeck Rasmussen – bioRxiv

Continuous glucose monitoring and intrapersonal variability in fasting glucose – Smadar Shilo – Nature Medicine

Animal microbiome

Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens – Seyed Hossien Kairmi – PlosOne

Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency – Naomi Sarpong – Frontiers in Microbiology

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience – Lauren F. Messer – Nature Communications

Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants – Zhe Pan – ISME Communications

Ocean microbiome

Decoding populations in the ocean microbiome – Ramiro Logares – Microbiome

Bioinformatics

High-resolution Profiling of Bacterial and Fungal Communities using Pangenome-Informed Taxon-Specific Long-Read Amplicons – Luzia Stalder – bioRxiv

CELEBRIMBOR: Pangenomes from metagenomes – Joel Hellewell – bioRxiv

April 10, 2024

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Good morning microbiome enthusiasts! Today’s MD is on the shorter side but we still have some really interesting articles picked out for you to peruse – including a microbiome-sparing targeted P. aeruginosa compound, effective probiotics for restoring a healthy coral microbiome, and a study characterizing the microbiome of metastatic cancers in over 4,000 biopsies. Plus, don’t forget that April’s Microbiome Virtual International Forum is happening next week!

Human Microbiome

Longitudinal multi-omics analysis uncovers the altered landscape of gut microbiota and plasma metabolome in response to high altitude – Yang Han et al – BMC Microbiome

Illuminating microflora: shedding light on the potential of blue light to modulate the cutaneous microbiome – Hannah J Serrage et al – Frontiers in Cellular and Infection Microbiology

Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC – Rauf Salamzade et al – Microbial Genomics

A pan-cancer analysis of the microbiome in metastatic cancer – Thomas Battaglia et al – Cell

A Lacticaseibacillus rhamnosus secretome induces immunoregulatory transcriptional, functional and immunometabolic signatures in human THP-1 monocytes – Michael P. Jeffrey et al – Nature Scientific Reports

The oral cavity and intestinal microbiome in children with functional constipation – Monika Kwiatkowska et al – Nature Scientific Reports

Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults – Casper S. Poulsen et al – Nature Scientific Reports

Colonization during a key developmental window reveals microbiota-dependent shifts in growth and immunity during undernutrition – Yadeliz A. Serrano Matos et al – BMC Microbiome

Animal models

Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice – Tatsuya Dokoshi et al – Nature Communications

A folate inhibitor exploits metabolic differences in Pseudomonas aeruginosa for narrow-spectrum targeting – Connor Chain et al – Nature Microbiology

Animal microbiome

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience – Lauren F. Messer et al – Nature Communications

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment – Nathalia Delgadillo-Ordoñez et al – Nature Communications Biology

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation – Daxi Wang et al – BMC Microbiome

Plant, root & soil microbiome

Root volatiles manipulate bacterial biofilms – Waseem Raza & Gaofei Jiang – Nature Ecology & Evolution

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community – Chong-Die Wu et al – BMC Plant Biology

Bioinformatics & tools

Holomics – a user-friendly R shiny application for multi-omics data integration and analysis – Katharina Munk et al – BMC Bioinformatics

March 7, 2024

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General microbiome

[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology

Studying mixed-species biofilms of Candida albicans and Staphylococcus aureus using evolutionary game theory – Dühring & Schuster – PLOS One

Human oral microbiome

Microbial Communities and Functional Genes in Periodontitis and Healthy Controls – Ma et al. – International Dental Journal

Human gut microbiome

[REVIEW]Unlocking the secrets: exploring the influence of the aryl hydrocarbon receptor and microbiome on cancer development – Rayan et al. – Cellular & Molecular Biology Letters

Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect – Lessard-Lord et al. – npj Biofilms and Microbiomes

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

Fecal microbiota impacts development of Cryptosporidium parvum in the mouse – Widmer & Creasey – Scientific reports

High fat diet is associated with gut microbiota dysbiosis and decreased gut microbial derived metabolites related to metabolic health in young Göttingen Minipigs – Lützhøft et al. – PLOS One

Animal microbiome (for animals in the wild)

Gustatory Responsiveness of Honey Bees Colonized with a Defined or Conventional Gut Microbiota – Suenami, Sato & Miyazaki – Microbes and Environments

[REVIEW]Fungal infection of insects: molecular insights and prospects – Hong et al. – Trends in Microbiology

Plant, root, and soil microbiome

Microbiome sequencing revealed the abundance of uncultured bacteria in the Phatthalung sago palm-growing soil – Nutaratat et al. – PLOS One

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

Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity – Angeles et al. – PLOS One

February 29, 2024

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Human oral microbiome

Using formalin fixed paraffin embedded tissue to characterize the microbiota in p16-positive and p16-negative tongue squamous cell carcinoma: a pilot study – Yuanbo et al. – BMC Oral Health

Human gut microbiome

Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota – Carasso et al. – Cell Host & Microbe

Integrated multi-omics analysis reveals gut microbiota dysbiosis and systemic disturbance in major depressive disorder – Xie et al. – Psychiatry Research

Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection – Nooij et al. – Genome Medicine

Bacteroides salyersiae is a potent chondroitin sulfate-degrading species in the human gut microbiota – Wang et al. – Microbiome

Elemental iron protects gut microbiota against oxygen-induced dysbiosis – Ostrov et al. PLOS One

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

Fecal microbiota transplantation ameliorates abdominal obesity through inhibiting microbiota-mediated intestinal barrier damage and inflammation in mice – Zhu et al. – Microbiological Research

Animal microbiome (for animals in the wild)

Exploring the modulatory effects of brown seaweed meal and extracts on intestinal microbiota and morphology of broiler chickens challenged with heat stress – Oretomiloye & Adewole – Poultry Science

Plant, root, and soil microbiome

Synthetic microbe-to-plant communication channels – Boo et al. Nature Communications

Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil – Li et al. – Microbiome

Influence of climatic variation on microbial communities during organic Pinot noir wine production – Ohwofasa et al. – PLOS One

February 23, 2024

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Today’s digest features the MetaPhlAn v4.1 & viral module, early life gut microbiome and diabetes, human milk oligosaccharides study, and more.

NEWS
MVIF has launched their crowdfunding campaign https://www.gofundme.com/f/me-mvif

See you at #MVIF next week!

Oral microbiome

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases – Davide Bazzani – npj Biofilms and Microbiomes

Nasal microbiome

Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Y Zhao – bioRxiv

Semen microbiome

Characterisation and comparison of semen microbiota and sperm function in men with infertility, recurrent miscarriage, or proven fertility – Shahriar Mowla – bioRxiv

Gut microbiome

CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei – Sivan Kijner – Nature Communications

Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study – Kinga Humińska-Lisowska – Plos One

The impact of iron supplementation on the preterm neonatal gut microbiome: A pilot study – Matthew VanOrmer – Plos One

Early-life exposures to specific commensal microbes prevent type 1 diabetes – Jamal Green – bioRxiv

Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing – Philipp Spohr – Scientific Reports

Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome – Qiyi Chen – Cell Host & Microbe

Animal experiment

The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice – Zhirui Cao – Nature Communications

Animal microbiome

Gut microbiome diversity and function during hibernation and spring emergence in an aquatic frog – Ji-Eun Lee – Plos One

Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages – Tao Zeng – bioRxiv

Water microbiome

A difficult coexistence: resolving the iron-induced nitrification delay in groundwater filters – Francesc Corbera-Rubio – bioRxiv

Human virome

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Moreno Zolfo – bioRxiv

February 21, 2024

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Human nasal microbiome

[PREPRINT]Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Zhao et al. – bioRxiv

Human oral microbiome

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases – Bazzani et al. – npj Biofilms and Microbiomes

Human gut microbiome

Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity – Behling et al. – Microbiome

Animal microbiome

Psychological stress-induced microbial metabolite indole-3-acetate disrupts intestinal cell lineage commitment – Wei et al. – Cell Metabolism

Gut microbiota contributes to bisphenol A-induced maternal intestinal and placental apoptosis, oxidative stress, and fetal growth restriction in pregnant ewe model by regulating gut-placental axis – Zhang et al. – Microbiome

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

Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones – Sun et al. – Microbiome

Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge – Li et al. – PeerJ

The exometabolome of microbial communities inhabiting bare ice surfaces on the southern Greenland Ice Sheet – Doting et al. – Environmental Microbiology

Searching for microbial contribution to micritization of shallow marine sediments – Garuglieri et al. – Environmental Microbiology

Food microbiology

Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing – Rana et al. – Scientific Reports

Phages and viruses

[PREPRINT]Fecal Virome Transplantation (FVT) from healthy humans remodels the gut bacteriome and virome and reduces metabolic syndrome in mice – Cervantes-Echeverría et al. – bioRxiv

[PREPRINT]Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Zolfo et al. – bioRxiv

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Why addressing how our brain and our gut talk to each other matter for IBS – Gut microbiota for health

December 6, 2023

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Human salivary microbiome

Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer – de Medeiros et al. – Microbiome

Human skin microbiome

[PREPRINT]Commensal skin bacteria exacerbate inflammation and delay skin healing – Khadka et al. – bioRxiv

Human vaginal microbiome

Integrating compositional and functional content to describe vaginal microbiomes in health and disease – Holm et al. – Microbiome

Comparison of vaginal microbiota between women with inflammatory bowel disease and healthy controls – Bar et al. – PLOS One

Human gut microbiome

Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics – Deng et al. – Microbiome

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

Vitamin D modulation of brain-gut-virome disorder caused by polystyrene nanoplastics exposure in zebrafish (Danio rerio) – Teng et al – Microbiome

Animal microbiome (for animals in the wild)

Diversity of gut microbiome in Rocky Mountainsnail across its native range – Chalifour, Elder & Li – PLOS One

[PREPRINT]Testing the effectiveness of a commercially sold probiotic on restoring the gut microbiota of honey bees: a field study – Damico et al. – bioRxiv

Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations – Lin et al. – Microbiome

Plant, root, and soil microbiome

Effects of multiple N, P, and K fertilizer combinations on strawberry growth and the microbial community – Bai et al. – PLOS One

Comparison of microbial community assemblages in the rhizosphere of three Amaranthus spp. – Chee-Sanford & Connor – PLOS One

Bioinformatics

Phantom oscillations in principal component analysis – Shinn – PNAS
This phenomenon is not new (e.g. know as horseshoe effect) but Shinn gives a very understandable explanation.

The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples – Heupink et al. – PLOS Computational Biology

[PREPRINT]metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis – Sun et al. – bioRxiv

[PREPRINT]MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics – Ma, Thairu & Sankaran

November 28, 2023

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Pregnancy and early life

[PREPRINT]Delivery mode impacts gut bacteriophage colonization during infancy – Subramanian et al. – medRxiv

Human oral microbiome

Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries – Alyousef et al. – BMC Oral Health

Human gut microbiome

Gastric coinfection with thiopeptide-positive Cutibacterium acnes decreases FOXM1 and pro-inflammatory biomarker expression in a murine model of Helicobacter pylori-induced gastric cancer – Lunger et al. – Microbiology Spectrum

[REVIEW]Butterflies in the gut: the interplay between intestinal microbiota and stress – Lai et al. – Journal of Biomedical Science

[REVIEW]Genetics, Nutrition, and Health: A New Frontier in Disease Prevention – Agrawal et al. – Journal of the American Nutrition Association

Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging – Sun et al. – Aging Cell

The changes of gut microbiota and metabolites in different drug-induced liver injuries – Zhu et al. – Journal of Medical Microbiology

[PREPRINT]The differing prevalences of propionate and butyrate producing bacteria in the human gut microbiota – Christensen et al. – bioRxiv

[PREPRINT]The Parkinson’s drug entacapone disrupts gut microbiome homeostasis via iron sequestration – Pereira et al. – bioRxiv

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

Mutual modulation of gut microbiota and the immune system in type 1 diabetes models – Rosell-Mases et al. – Nature Communications

[PREPRINT]Microbiota-dependent early life programming of gastrointestinal motility – Frith et al. – bioRxiv

Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis – Gurczynski et al. – JCI insight

High-altitude and low-altitude adapted chicken gut-microbes have different functional diversity – Bhagat et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Introducing an environmental microbiome to axenic Aedes aegypti mosquitoes documents bacterial responses to a blood meal – LaReau et al. – Applied and Environmental Microbiology

Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer – Zhuang et al. – Microbiology Spectrum

Plant, root, and soil microbiome

[PREPRINT]Global patterns in gene content of soil microbiomes emerge from microbial interactions – Crocker et al. – bioRxiv

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

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India – Brar et al. – Journal of Genetic Engineering and Biotechnology

Bioinformatics

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data – Padron-Manrique et al. – Bioinformatics

Facilitating bioinformatics reproducibility with QIIME 2 provenance Replay – Keefe et al. – PLOS Computational Biology

Techniques

High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ – Jin, Yamamoto & Shiroguchi