ArticlePeerJ2017
A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 32 citations in OpenAlex.
- Systematic Categorization and Functional Diversity of Secondary Metabolites from Bacillus spp.: A Review.Probiotics and antimicrobial proteins · 2026Review
- Sulfur-Containing Microbial Natural Products and Their Role in Communal Interactions.Journal of natural products · 2025Review
- Antimicrobial peptides: natural templates for next-generation therapeutics against antimicrobial resistance.Frontiers in cellular and infection microbiology · 2025Review
- Does gut microbiota dysbiosis impact the metabolic alterations of hydrogen sulfide and lanthionine in patients with chronic kidney disease?BMC microbiology · 2024Article
- Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota.Microbial ecology · 2023Review
- Classification and Multifaceted Potential of Secondary Metabolites Produced byMolecules (Basel, Switzerland) · 2023Review
- Network Science and Group Fusion Similarity-Based Searching to Explore the Chemical Space of Antiparasitic Peptides.ACS omega · 2022Article
- Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern.Frontiers in microbiology · 2022Article
- Challenges and advances in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs).Synthetic and systems biotechnology · 2020Review
- Gut microbiota as a source of novel antimicrobials.Gut microbes · 2019Review
- Metabolic phenotyping of the human microbiome.F1000Research · 2019Review
- Publisher Correction: The gut-liver axis and the intersection with the microbiome.Nature reviews. Gastroenterology & hepatology · 2018Article
- Secondary metabolite production and the safety of industrially important members of the Bacillus subtilis group.FEMS microbiology reviews · 2018Review
- The gut-liver axis and the intersection with the microbiome.Nature reviews. Gastroenterology & hepatology · 2018Review
- Butyrate Protects Mice Against Methionine-Choline-Deficient Diet-Induced Non-alcoholic Steatohepatitis by Improving Gut Barrier Function, Attenuating Inflammation and Reducing Endotoxin Levels.Frontiers in microbiology · 2018Article
- High Throughput Identification of Antimicrobial Peptides from Fish Gastrointestinal Microbiota.Toxins · 2017Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the density and distribution of the subclass I lantibiotic modification protein, LanB, in human oral and stool microbiome datasets using a specially constructed profile Hidden Markov Model (HMM).
methodsThe model was validated by correctly identifying known lanB genes in the genomes of known bacteriocin producers more effectively than other methods, while being sensitive enough to differentiate between different subclasses of lantibiotic modification proteins. This approach was compared with two existing methods to screen both genomic and metagenomic datasets obtained from the Human Microbiome Project (HMP).
resultsOf the methods evaluated, the new profile HMM identified the greatest number of putative LanB proteins in the stool and oral metagenome data while BlastP identified the fewest. In addition, the model identified more LanB proteins than a pre-existing Pfam lanthionine dehydratase model. Searching the gastrointestinal tract subset of the HMP reference genome database with the new HMM identified seven putative subclass I lantibiotic producers, including two members of the Coprobacillus genus.
conclusionsThese findings establish custom profile HMMs as a potentially powerful tool in the search for novel bioactive producers with the power to benefit human health, and reinforce the repertoire of apparent bacteriocin-encoding gene clusters that may have been overlooked by culture-dependent mining efforts to date.
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