Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures

Abstract

The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbohydrate degrading enzymes (CAZymes) that have a high potential for future applications. Green microbial mat, predominantly photosynthetic bacteria, was attached to submerged or floating leaves litter. At the spring head, the sediment mixture consisted of plant debris, predominantly brownish-reddish gelatinous microbial mat, pale tan biofilm, and grey-white filament biofilm. The population in the spring head had a higher percentage of archaea and hyperthermophiles than the green mat. Concurrently, we cataloged nearly 10,000 sequences of CAZymes in both green and brown biofilms using the shotgun metagenomic sequencing approach. These sequences include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α-l-arabinofuranosidase, and other CAZymes. In conclusion, this work elucidated that SKY is a unique hot spring due to its rich lignocellulosic material, often absent in other hot springs. The data collected from this study serves as a repository of new thermostable macromolecules, in particular families of glycoside hydrolases.

'Targeting' the search: An upgraded structural and functional repository of antimicrobial peptides for biofilm studies (B-AMP v2.0) with a focus on biofilm protein targets

“…This is a limitation, given that AMPs are known to target bacterial components such as surface lipids (AMP-lipid interactions are involved in membrane disruption) and polysaccharides, that are also known to play a role in biofilm formation ( Hollmann et al., 2018 ; Benfield and Henriques, 2020 ; Lin et al., 2020 ; Zhang et al., 2021 ). Future expansions of B-AMP v2.0 can include bacterial lipid and lipoprotein targets from databases such as LIPID MAPS Consortium and DOLOP, and bacterial carbohydrates using Polysac DB, Bacterial CSDB, and CAZy ( ) ( LIPID MAPS ® lipidomics gateway ; Babu et al., 2006 ; Onyango et al., 2021 ; Leggieri et al., 2022 ; Liew et al., 2022 ). An additional limitation in B-AMP v2.0 is that the targets represent only bacterial targets (no fungal targets), and 3D structural models are not available for all biofilm targets.…”

‘Targeting’ the Search: An Upgraded Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies (B-AMP v2.0) with a Focus on Biofilm Protein Targets

“…This is a limitation, given that AMPs are known to target bacterial components such as surface lipids (AMP-lipid interactions are involved in membrane disruption) and polysaccharides, that are also known to play a role in biofilm formation (Hollmann et al, 2018; Benfield and Henriques, 2020; Lin et al, 2020; Zhang et al, 2021). Future expansions of B-AMP v2.0 can include bacterial lipid and lipoprotein targets from databases such as LIPID MAPS Consortium and DOLOP, and bacterial carbohydrates using Polysac DB, Bacterial CSDB, and CAZy (www.cazy.org/) (LIPID MAPS® Lipidomics Gateway; Babu et al, 2006; Onyango et al, 2021; Leggieri et al, 2022; Liew et al, 2022). An additional limitation in B-AMP v2.0 is that the targets represent only bacterial targets (no fungal targets), and 3D structural models are not available for all biofilm targets.…”

The Role of Feeding Characteristics in Shaping Gut Microbiota Composition and Function of Ensifera (Orthoptera)

“…UpSet analysis (threshold > 0.1) was used to show each sample’s shared and unique microorganism. Unigenes were compared with the KEGG [ 51 ] and CAZymes databases [ 52 , 53 ] (blastp, evalue ≤ 1 × 10 −5 ) to obtain the annotation enrichment of each database. The statistical analysis was carried out by pairwise comparisons with Welch’s t -test [ 54 ] at KEGG levels 1 and 2, and CAZy level 2, with p < 0.05 as a significant difference.…”