scholarly journals Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis.

2020 ◽  
Author(s):  
Asimenia Gavriilidou ◽  
Johanna Gutleben ◽  
Dennis Versluis ◽  
Francesca Forgiarini ◽  
Mark WJ van Passel ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Carbohydrate Metabolism ◽  
Secondary Metabolite ◽  
Gene Clusters ◽  
Gliding Motility ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Secondary Metabolite Biosynthesis

Abstract BackgroundMembers of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity. ResultsComparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes support the capacity of marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes. Notably, not all gliding bacteria formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains.ConclusionsOur study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.

scholarly journals Comparative genomics analysis of Chryseobacterium sp. KMC2 reveals metabolic pathways involved in keratinous utilization and natural product biosynthesis

2021 ◽  
Author(s):  
Dingrong Kang ◽  
Saeed Shoaie ◽  
Samuel Jacquiod ◽  
Søren Johannes Sørensen ◽  
Rodrigo Ledesma-Amaro
Keyword(s):  
Secondary Metabolite ◽  
Metabolic Pathways ◽  
Genome Mining ◽  
Renewable Resource ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Microbial Conversion ◽  
Metabolic Potential ◽  
A Genome ◽  
Keratinous Materials

Several efforts have been made to valorize keratinous materials, an abundant and renewable resource. Despite these attempts to valorize products generated from keratin hydrolysate, either via chemical or microbial conversion, they generally remain with an overall low value. In this study, a promising keratinolytic strain from the genus Chryseobacterium (Chryseobacteriumsp. KMC2) was investigated using comparative genomic tools against publicly available reference genomes to reveal the metabolic potential for biosynthesis of valuable secondary metabolites. Genome and metabolic features of four species were compared, shows different gene numbers but similar functional categories. We successfully mined eleven different secondary metabolite gene clusters of interest from the four genomes, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, all showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium spp. and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, providing alternatives to valorize keratinous materials into high-value natural products.

scholarly journals Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production

2021 ◽  
Vol 9 (5) ◽  
pp. 1042
Author(s):  
Dingrong Kang ◽  
Saeed Shoaie ◽  
Samuel Jacquiod ◽  
Søren J. Sørensen ◽  
Rodrigo Ledesma-Amaro
Keyword(s):  
Secondary Metabolite ◽  
Genome Mining ◽  
Tca Cycle ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Bioactive Natural Products ◽  
A Genome ◽  
Genomic Tools ◽  
Keratinous Materials

A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium species and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products.

An atlas of bacterial secondary metabolite biosynthesis gene clusters

2021 ◽  
Author(s):  
Bin Wei ◽  
Ao‐Qi Du ◽  
Zhen‐Yi Zhou ◽  
Cong Lai ◽  
Wen‐Chao Yu ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Gene Clusters ◽  
Biosynthesis Gene ◽  
Secondary Metabolite Biosynthesis

scholarly journals antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

2011 ◽  
Vol 39 (suppl_2) ◽  
pp. W339-W346 ◽  
Author(s):  
Marnix H. Medema ◽  
Kai Blin ◽  
Peter Cimermancic ◽  
Victor de Jager ◽  
Piotr Zakrzewski ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Gene Clusters ◽  
Rapid Identification ◽  
Fungal Genome ◽  
Genome Sequences ◽  
Biosynthesis Gene ◽  
Secondary Metabolite Biosynthesis

scholarly journals Alterations in the Porcine Colon Microbiota Induced by the Gastrointestinal Nematode Trichuris suis

2012 ◽  
Vol 80 (6) ◽  
pp. 2150-2157 ◽  
Author(s):  
Robert W. Li ◽  
Sitao Wu ◽  
Weizhong Li ◽  
Karl Navarro ◽  
Robin D. Couch ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Parasitic Infection ◽  
Proximal Colon ◽  
Lysine Biosynthesis ◽  
Intestinal Lumen ◽  
Rrna Gene ◽  
Significant Shift ◽  
Metabolic Potential ◽  
Content Type ◽  
Trichuris Suis

ABSTRACTHelminth parasites ensure their survival by regulating host immunity through mechanisms that dampen inflammation. These properties have recently been exploited therapeutically to treat human diseases. The biocomplexity of the intestinal lumen suggests that interactions between the parasite and the intestinal microbiota would also influence inflammation. In this study, we characterized the microbiota in the porcine proximal colon in response toTrichuris suis(whipworm) infection using 16S rRNA gene-based and whole-genome shotgun (WGS) sequencing. A 21-dayT. suisinfection in four pigs induced a significant change in the composition of the proximal colon microbiota compared to that of three parasite-naive pigs. Among the 15 phyla identified, the abundances ofProteobacteriaandDeferribactereswere changed in infected pigs. The abundances of approximately 13% of genera were significantly altered by infection. Changes in relative abundances ofSuccinivibrioandMucispirillum, for example, may relate to alterations in carbohydrate metabolism and niche disruptions in mucosal interfaces induced by parasitic infection, respectively. Of note, infection byT. suisled to a significant shift in the metabolic potential of the proximal colon microbiota, where 26% of all metabolic pathways identified were affected. Besides carbohydrate metabolism, lysine biosynthesis was repressed as well. A metabolomic analysis of volatile organic compounds (VOCs) in the luminal contents showed a relative absence in infected pigs of cofactors for carbohydrate and lysine biosynthesis, as well as an accumulation of oleic acid, suggesting altered fatty acid absorption contributing to local inflammation. Our findings should facilitate development of strategies for parasitic control in pigs and humans.

scholarly journals Increased abundance of secreted hydrolytic enzymes and secondary metabolite gene clusters define the genomes of latent plant pathogens in the Botryosphaeriaceae

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jan H. Nagel ◽  
Michael J. Wingfield ◽  
Bernard Slippers
Keyword(s):  
Secondary Metabolite ◽  
Plant Pathogens ◽  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Biosynthetic Gene ◽  
Plant Interactions ◽  
Biosynthetic Gene Clusters ◽  
Genome Analyses

Abstract Background The Botryosphaeriaceae are important plant pathogens, but also have the ability to establish asymptomatic infections that persist for extended periods in a latent state. In this study, we used comparative genome analyses to shed light on the genetic basis of the interactions of these fungi with their plant hosts. For this purpose, we characterised secreted hydrolytic enzymes, secondary metabolite biosynthetic gene clusters and general trends in genomic architecture using all available Botryosphaeriaceae genomes, and selected Dothideomycetes genomes. Results The Botryosphaeriaceae genomes were rich in carbohydrate-active enzymes (CAZymes), proteases, lipases and secondary metabolic biosynthetic gene clusters (BGCs) compared to other Dothideomycete genomes. The genomes of Botryosphaeria, Macrophomina, Lasiodiplodia and Neofusicoccum, in particular, had gene expansions of the major constituents of the secretome, notably CAZymes involved in plant cell wall degradation. The Botryosphaeriaceae genomes were shown to have moderate to high GC contents and most had low levels of repetitive DNA. The genomes were not compartmentalized based on gene and repeat densities, but genes of secreted enzymes were slightly more abundant in gene-sparse regions. Conclusion The abundance of secreted hydrolytic enzymes and secondary metabolite BGCs in the genomes of Botryosphaeria, Macrophomina, Lasiodiplodia, and Neofusicoccum were similar to those in necrotrophic plant pathogens and some endophytes of woody plants. The results provide a foundation for comparative genomic analyses and hypotheses to explore the mechanisms underlying Botryosphaeriaceae host-plant interactions.

scholarly journals Insights into the cultured bacterial fraction of corals

2020 ◽  
Author(s):  
Michael Sweet ◽  
Helena Villela ◽  
Tina Keller-Costa ◽  
Rodrigo Costa ◽  
Stefano Romano ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Comprehensive Overview ◽  
Associated Bacteria ◽  
Reef Restoration ◽  
Coral Holobiont ◽  
Metabolic Interactions ◽  
And Function

Abstract Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite the putative importance of bacteria, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable, coral-associated bacteria. A total of 3055 isolates from 52 studies were considered by our meta-survey. Of these, 1045 had full length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterial-coral symbioses among them. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features - not previously described for coral-bacterial symbioses - involved in host colonization and host-symbiont recognition, antiviral defence mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning, and guide the selection of probiotic candidates to promote coral resilience and improve reef restoration efforts.

scholarly journals Divergence of pigments in three phylogenetically close Monascus species (M. pilosus, M. ruber, and M. purpureus) based on secondary metabolite biosynthetic gene clusters

2020 ◽  
Author(s):  
YUKI HIGA ◽  
Young-Soo Kim ◽  
Md. Altaf-Ul-Amin ◽  
Ming Huan ◽  
Naoaki Ono ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Food Industry ◽  
Gene Clusters ◽  
Illumina Miseq ◽  
Biosynthetic Gene ◽  
Asian Countries ◽  
Biosynthetic Gene Clusters ◽  
Natural Pigments ◽  
Secondary Metabolite Biosynthesis ◽  
Paired End Sequencing

Abstract Background: Species under the genus Monascus are considered as economically important and have been widely used in the production of yellow and red food colorants. In particular, three Monascus species, namely, M. pilosus , M. purpureus , and M. ruber , are used for food fermentation in the cuisine of East Asian countries such as China, Japan, and Korea. These species have also been utilized in the production of various kinds of natural pigments. Results: We examined the diversity of pigment-related biosynthetic pathways in three Monascus species ( M. pilosus , M. purpureus , and M. ruber ) at the metabolome and genome levels. Illumina MiSeq 300 bp paired-end sequencing generated 17 million high-quality short reads in each species, corresponding to 200 times the genome size. We measured the pigments and their related metabolites using potato dextrose liquid (PDL) media. The colors in the PDL media corresponding to the pigments and their related metabolites produced by the three species are very different from each other. The gene clusters for secondary metabolite biosynthesis of the three Monascus species also diverged, confirming that M. pilosus and M. purpureus are chemotaxonomically different. M. ruber has similar biosynthetic gene clusters for citrinin, monacolin K, and Monascus azaphilone pigments with M. pilosus and M. purpureus. The comparison of secondary metabolites produced also revealed divergence in the three species. Conclusions: Our findings are important for improving the utilization of Monascus species in the food industry and industrial field. However, in view of food safety, we need to determine if the toxins produced by some Monascus strains exist in the genome or in the metabolome.

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