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

Liew, Kok Jun; Liang, Chee Hung; Lau, Yee Ting; Yaakop, Amira Suriaty; Chan, Kok‐Gan; Shahar, Saleha; Shamsir, Mohd Shahir; Goh, Kian Mau

doi:10.1038/s41598-022-06943-9

Cited by 22 publications

(22 citation statements)

References 72 publications

(84 reference statements)

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“…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.…”

Section: Discussionmentioning

confidence: 99%

'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

Ravichandran

Avatapalli²,

Narasimhan³

et al. 2022

Front. Cell. Infect. Microbiol.

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Bacterial biofilms, often as multispecies communities, are recalcitrant to conventional antibiotics, making the treatment of biofilm infections a challenge. There is a push towards developing novel anti-biofilm approaches, such as antimicrobial peptides (AMPs), with activity against specific biofilm targets. In previous work, we developed Biofilm-AMP, a structural and functional repository of AMPs for biofilm studies (B-AMP v1.0) with more than 5000 structural models of AMPs and a vast library of AMP annotations to existing biofilm literature. In this study, we present an upgraded version of B-AMP, with a focus on existing and novel bacterial biofilm targets. B-AMP v2.0 hosts a curated collection of 2502 biofilm protein targets across 473 bacterial species, with structural protein models and functional annotations from PDB, UniProt, and PubMed databases. The biofilm targets can be searched for using the name of the source organism, and function and type of protein, and results include designated Target IDs (unique to B-AMP v2.0), UniProt IDs, 3D predicted protein structures, PDBQT files, pre-defined protein functions, and relevant scientific literature. To present an example of the combined applicability of both, the AMP and biofilm target libraries in the repository, we present two case studies. In the first case study, we expand an in silico pipeline to evaluate AMPs against a single biofilm target in the multidrug resistant, bacterial pathogen Corynebacterium striatum, using 3D protein-peptide docking models from previous work and Molecular Dynamics simulations (~1.2µs). In the second case study, we build an in silico pipeline to identify candidate AMPs (using AMPs with both anti-Gram positive and anti-Gram negative activity) against two biofilm targets with a common functional annotation in Pseudomonas aeruginosa and Staphylococcus aureus, widely-encountered bacterial co-pathogens. With its enhanced structural and functional capabilities, B-AMP v2.0 serves as a comprehensive resource for AMP investigations related to biofilm studies. B-AMP v2.0 is freely available at https://b-amp.karishmakaushiklab.com and will be regularly updated with structural models of AMPs and biofilm targets, as well as 3D protein-peptide interaction models for key biofilm-forming pathogens.

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Section: Discussionmentioning

confidence: 99%

'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

Ravichandran

Avatapalli²,

Narasimhan³

et al. 2022

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

show abstract

“…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.…”

Section: Discussionmentioning

confidence: 99%

‘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

Ravichandran

Avatapalli

Narasimhan

et al. 2022

Preprint

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Bacterial biofilms, often as multispecies communities, are recalcitrant to conventional antibiotics, making the treatment of biofilm infections a challenge. There is a push towards developing novel anti-biofilm approaches, such as antimicrobial peptides (AMPs), with activity against specific biofilm targets. In previous work, we developed Biofilm-AMP, a structural and functional repository of AMPs for biofilm studies (B-AMP v1.0) with more than 5000 structural models of AMPs and a vast library of AMP annotations to existing biofilm literature. In this study, we present an upgraded version of B-AMP, with a focus on existing and novel bacterial biofilm targets. B-AMP v2.0 hosts a curated collection of 2502 biofilm protein targets across 473 bacterial species, with structural protein models and functional annotations from PDB, UniProt, and PubMed databases. The biofilm targets can be searched for using the name of the source organism, and function and type of protein, and results include designated Target IDs (unique to B-AMP v2.0), UniProt IDs, 3D predicted protein structures, PDBQT files, pre-defined protein function, and relevant scientific literature. To present an example of the combined applicability of both, the AMP and biofilm target libraries in the repository, we present two case studies. In the first case study, we expand an in silico pipeline to evaluate AMPs against a single biofilm target in the multidrug resistant, bacterial pathogen Corynebacterium striatum, using 3D protein-peptide docking models from previous work and Molecular Dynamics simulations (~1.18 microseconds). In the second case study, we build an in silico pipeline to identify candidate AMPs (using AMPs with both anti-Gram positive and anti-Gram negative activity) against two biofilm targets with a common functional classification in Pseudomonas aeruginosa and Staphylococcus aureus, widely-encountered bacterial co-pathogens. With its enhanced structural and functional capabilities, B-AMP v2.0 serves as a comprehensive resource for AMP investigations related to biofilm studies. B-AMP v2.0 is freely available at https://b-amp.karishmakaushiklab.com and will be regularly updated with structural models of AMPs and biofilm targets, as well as 3D protein-peptide interaction models for key biofilm-forming pathogens.

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“…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.…”

Section: Methodsmentioning

confidence: 99%

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

Zhu

Meng

et al. 2022

Insects

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Feeding habits were the primary factor affecting the gut bacterial communities in Ensifera. However, the interaction mechanism between the gut microbiota and feeding characteristics is not precisely understood. Here, the gut microbiota of Ensifera with diverse feeding habits was analyzed by shotgun metagenomic sequencing to further clarify the composition and function of the gut microbiota and its relationship with feeding characteristics. Our results indicate that under the influence of feeding habits, the gut microbial communities of Ensifera showed specific characteristics. Firstly, the gut microbial communities of the Ensifera with different feeding habits differed significantly, among which the gut microbial diversity of the herbivorous Mecopoda niponensis was the highest. Secondly, the functional genes related to feeding habits were in high abundance. Thirdly, the specific function of the gut microbial species in the omnivorous Gryllotalpa orientalis showed that the more diverse the feeding behavior of Ensifera, the worse the functional specificity related to the feeding characteristics of its gut microbiota. However, feeding habits were not the only factors affecting the gut microbiota of Ensifera. Some microorganisms’ genes, whose functions were unrelated to feeding characteristics but were relevant to energy acquisition and nutrient absorption, were detected in high abundance. Our results were the first to report on the composition and function of the gut microbiota of Ensifera based on shotgun metagenomic sequencing and to explore the potential mechanism of the gut microbiota’s association with diverse feeding habits.

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

Cited by 22 publications

References 72 publications

'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

'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

‘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

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

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