Pub Date : 2024-09-19eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1443195
B R Ajesh, R Sariga, S Nakkeeran, P Renukadevi, N Saranya, Saad Alkahtani
Introduction: Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), poses a significant global threat to banana cultivation. Conventional methods of disease management are increasingly challenged, thus making it necessary to explore alternative strategies. Bacterial endophytes, particularly from resistant genotypes, are gaining attention as potential biocontrol agents. Sphingobacterium thalpophilum, isolated from the resistant banana cultivar Pisang lilin (JALHSB010000001-JALHSB010000029), presents an intriguing prospect for combating Fusarium wilt. However, its underlying biocontrol mechanisms remain poorly understood. This study aimed to elucidate the antifungal efficacy of S. thalpophilum NMS02 S296 against Foc and explore its biocontrol mechanisms at the genomic level.
Methods: Whole genome sequencing of S. thalpophilum NMS02 S296 was conducted using next-generation sequencing technologies and bioinformatics analyses were performed to identify genes associated with antifungal properties. In vitro assays were used to assess the inhibitory effects of the bacterial isolate on the mycelial growth of Foc. To explore the biomolecules responsible for the observed antagonistic activity, metabolites diffused into the agar at the zone of inhibition between Foc S16 and S. thalpophilum NMS02 S296 were extracted and identified.
Results: Whole genome sequencing revealed an array of genes encoding antifungal enzymes and secondary metabolites in S. thalpophilum NMS02 S296. In vitro experiments demonstrated significant inhibition of Foc mycelial growth by the bacterial endophyte. Comparative genomic analysis highlighted unique genomic features in S. thalpophilum linked to its biocontrol potential, setting it apart from other bacterial species.
Discussion: The study underscores the remarkable antifungal efficacy of S. thalpophilum NMS02 S296 against Fusarium wilt. The genetic basis for its biocontrol potential was elucidated through whole genome sequencing, shedding light on the mechanisms behind its antifungal activity. This study advanced our understanding of bacterial endophytes as biocontrol agents and offers a promising avenue for plant growth promotion towards sustainable strategies to mitigate Fusarium wilt in banana cultivation.
导言:由 Fusarium oxysporum f. sp. cubense(Foc)引起的镰刀菌枯萎病对全球香蕉种植构成了重大威胁。传统的病害防治方法受到越来越多的挑战,因此有必要探索替代策略。细菌内生菌,尤其是来自抗病基因型的细菌内生菌,作为潜在的生物控制剂正受到越来越多的关注。从抗性香蕉栽培品种 Pisang lilin(JALHSB010000001-JALHSB010000029)中分离出的 Sphingobacterium thalpophilum 为防治镰刀菌枯萎病带来了令人感兴趣的前景。然而,人们对其潜在的生物防治机制仍然知之甚少。本研究旨在阐明 S. thalpophilum NMS02 S296 对镰刀菌的抗真菌功效,并从基因组水平探索其生物防治机制:方法:利用下一代测序技术对嗜硫菌 NMS02 S296 进行全基因组测序,并进行生物信息学分析,以确定与抗真菌特性相关的基因。体外试验用于评估细菌分离物对 Foc 菌丝生长的抑制作用。为了探索导致观察到的拮抗活性的生物大分子,提取并鉴定了扩散到 Foc S16 与 S. thalpophilum NMS02 S296 之间抑制区琼脂中的代谢物:结果:全基因组测序揭示了嗜沙蚕 NMS02 S296 中一系列编码抗真菌酶和次级代谢产物的基因。体外实验表明,细菌内生菌对 Foc 菌丝生长有明显的抑制作用。比较基因组分析凸显了 S. thalpophilum 与其生物防治潜力相关的独特基因组特征,使其有别于其他细菌物种:本研究强调了 S. thalpophilum NMS02 S296 对镰刀菌枯萎病的显著抗真菌功效。通过全基因组测序,阐明了其生物防治潜力的遗传基础,揭示了其抗真菌活性背后的机制。这项研究加深了我们对细菌内生菌作为生物控制剂的认识,并为促进植物生长、采取可持续策略减轻香蕉镰刀菌枯萎病提供了一条前景广阔的途径。
{"title":"Insights on mining the pangenome of <i>Sphingobacterium thalpophilum</i> NMS02 S296 from the resistant banana cultivar <i>Pisang lilin</i> confirms the antifungal action against <i>Fusarium oxysporum</i> f. sp. <i>cubense</i>.","authors":"B R Ajesh, R Sariga, S Nakkeeran, P Renukadevi, N Saranya, Saad Alkahtani","doi":"10.3389/fmicb.2024.1443195","DOIUrl":"10.3389/fmicb.2024.1443195","url":null,"abstract":"<p><strong>Introduction: </strong><i>Fusarium</i> wilt, caused by <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> (<i>Foc</i>), poses a significant global threat to banana cultivation. Conventional methods of disease management are increasingly challenged, thus making it necessary to explore alternative strategies. Bacterial endophytes, particularly from resistant genotypes, are gaining attention as potential biocontrol agents. <i>Sphingobacterium thalpophilum</i>, isolated from the resistant banana cultivar <i>Pisang lilin</i> (JALHSB010000001-JALHSB010000029), presents an intriguing prospect for combating <i>Fusarium</i> wilt. However, its underlying biocontrol mechanisms remain poorly understood. This study aimed to elucidate the antifungal efficacy of <i>S. thalpophilum</i> NMS02 S296 against <i>Foc</i> and explore its biocontrol mechanisms at the genomic level.</p><p><strong>Methods: </strong>Whole genome sequencing of <i>S. thalpophilum</i> NMS02 S296 was conducted using next-generation sequencing technologies and bioinformatics analyses were performed to identify genes associated with antifungal properties. <i>In vitro</i> assays were used to assess the inhibitory effects of the bacterial isolate on the mycelial growth of <i>Foc</i>. To explore the biomolecules responsible for the observed antagonistic activity, metabolites diffused into the agar at the zone of inhibition between <i>Foc</i> S16 and <i>S. thalpophilum</i> NMS02 S296 were extracted and identified.</p><p><strong>Results: </strong>Whole genome sequencing revealed an array of genes encoding antifungal enzymes and secondary metabolites in <i>S. thalpophilum</i> NMS02 S296. In vitro experiments demonstrated significant inhibition of <i>Foc</i> mycelial growth by the bacterial endophyte. Comparative genomic analysis highlighted unique genomic features in <i>S. thalpophilum</i> linked to its biocontrol potential, setting it apart from other bacterial species.</p><p><strong>Discussion: </strong>The study underscores the remarkable antifungal efficacy of <i>S. thalpophilum</i> NMS02 S296 against <i>Fusarium</i> wilt. The genetic basis for its biocontrol potential was elucidated through whole genome sequencing, shedding light on the mechanisms behind its antifungal activity. This study advanced our understanding of bacterial endophytes as biocontrol agents and offers a promising avenue for plant growth promotion towards sustainable strategies to mitigate <i>Fusarium</i> wilt in banana cultivation.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11446778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Two physical treatments (heat via water bath and cold air) with various temperatures (20/70/75/80°C and - 80/-90°C) and exposure times (20, 30, 40 s) were carried out to identify a decontaminating effect on zoonotic pathogens on broiler carcasses. Subsequently, carcasses were analyzed for thermotolerant Campylobacter (C.), Salmonella, Escherichia (E.). coli and total colony count (TCC). Moreover, for the hot water treatment, qPCR with viable/dead differentiation (v-qPCR) was applied to detect viable but non-culturable cells (VBNC) of Campylobacter, referred to as intact but putatively infectious units (IPIU). Hot water immersion was tested on carcasses inoculated with C. jejuni and Salmonella, while cold air treatment was evaluated for naturally contaminated carcasses of broiler flocks colonized with Campylobacter. For hot water treatment, the statistically significant reducing effect was about 1 log10 CFU/ml for both Salmonella and Campylobacter for 70-80°C and 20/30 s treatments. The effect of heat treatment for Campylobacter was smaller when samples were analyzed with v-qPCR with reductions of 0.5-0.8 log10 IPIU/ml in mean. Cold air treatments at -90°C were effective in reducing the mean contamination level of Campylobacter by 0.4-0.5 log10 CFU/ml at all exposure times (p < 0.05). Hot water treatments showed a decreasing trend on TCC by 0.6-0.9 log10 CFU/ml (p < 0.05). TCC counts were not significantly affected by cold air treatment. For E. coli no statistically significant reductions were observed by hot water treatment. The cold air treatment at -90°C for 20 and 40 s led to a reduction of E. coli by 0.4 and 0.8 log10 CFU/ml (p < 0.05), respectively. Treatment of carcasses with higher bacterial levels tended to show higher reduction. The research demonstrated that the efficacy of physical treatments for decontamination of broiler carcasses was more pronounced for hot water immersion than for cold air exposure. In conclusion, the results shed light on the potential application of these physical treatments in practice to reduce the quantitative load of contaminating pathogens to enhance food safety in the broiler meat production.
{"title":"Application of hot water and cold air to reduce bacterial contamination on broiler carcasses.","authors":"Anja Beterams, Alina Kirse, Lothar Kreienbrock, Kerstin Stingl, Niels Bandick, Felix Reich","doi":"10.3389/fmicb.2024.1429756","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1429756","url":null,"abstract":"<p><p>Two physical treatments (heat via water bath and cold air) with various temperatures (20/70/75/80°C and - 80/-90°C) and exposure times (20, 30, 40 s) were carried out to identify a decontaminating effect on zoonotic pathogens on broiler carcasses. Subsequently, carcasses were analyzed for thermotolerant <i>Campylobacter (C.)</i>, <i>Salmonella</i>, <i>Escherichia (E.). coli</i> and total colony count (TCC). Moreover, for the hot water treatment, qPCR with viable/dead differentiation (v-qPCR) was applied to detect viable but non-culturable cells (VBNC) of <i>Campylobacter,</i> referred to as intact but putatively infectious units (IPIU). Hot water immersion was tested on carcasses inoculated with <i>C. jejuni</i> and <i>Salmonella</i>, while cold air treatment was evaluated for naturally contaminated carcasses of broiler flocks colonized with <i>Campylobacter</i>. For hot water treatment, the statistically significant reducing effect was about 1 log<sub>10</sub> CFU/ml for both <i>Salmonella</i> and <i>Campylobacter</i> for 70-80°C and 20/30 s treatments. The effect of heat treatment for <i>Campylobacter</i> was smaller when samples were analyzed with v-qPCR with reductions of 0.5-0.8 log<sub>10</sub> IPIU/ml in mean. Cold air treatments at -90°C were effective in reducing the mean contamination level of <i>Campylobacter</i> by 0.4-0.5 log<sub>10</sub> CFU/ml at all exposure times (<i>p</i> < 0.05). Hot water treatments showed a decreasing trend on TCC by 0.6-0.9 log<sub>10</sub> CFU/ml (p < 0.05). TCC counts were not significantly affected by cold air treatment. For <i>E. coli</i> no statistically significant reductions were observed by hot water treatment. The cold air treatment at -90°C for 20 and 40 s led to a reduction of <i>E. coli</i> by 0.4 and 0.8 log<sub>10</sub> CFU/ml (<i>p</i> < 0.05), respectively. Treatment of carcasses with higher bacterial levels tended to show higher reduction. The research demonstrated that the efficacy of physical treatments for decontamination of broiler carcasses was more pronounced for hot water immersion than for cold air exposure. In conclusion, the results shed light on the potential application of these physical treatments in practice to reduce the quantitative load of contaminating pathogens to enhance food safety in the broiler meat production.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-19eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1450804
Miki Ikebe, Kota Aoki, Mitsuko Hayashi-Nishino, Chikara Furusawa, Kunihiko Nishino
Although it is well known that the morphology of Gram-negative rods changes on exposure to antibiotics, the morphology of antibiotic-resistant bacteria in the absence of antibiotics has not been widely investigated. Here, we studied the morphologies of 10 antibiotic-resistant strains of Escherichia coli and used bioinformatics tools to classify the resistant cells under light microscopy in the absence of antibiotics. The antibiotic-resistant strains showed differences in morphology from the sensitive parental strain, and the differences were most prominent in the quinolone-and β-lactam-resistant bacteria. A cluster analysis revealed increased proportions of fatter or shorter cells in the antibiotic-resistant strains. A correlation analysis of morphological features and gene expression suggested that genes related to energy metabolism and antibiotic resistance were highly correlated with the morphological characteristics of the resistant strains. Our newly proposed deep learning method for single-cell classification achieved a high level of performance in classifying quinolone-and β-lactam-resistant strains.
{"title":"Bioinformatic analysis reveals the association between bacterial morphology and antibiotic resistance using light microscopy with deep learning.","authors":"Miki Ikebe, Kota Aoki, Mitsuko Hayashi-Nishino, Chikara Furusawa, Kunihiko Nishino","doi":"10.3389/fmicb.2024.1450804","DOIUrl":"10.3389/fmicb.2024.1450804","url":null,"abstract":"<p><p>Although it is well known that the morphology of Gram-negative rods changes on exposure to antibiotics, the morphology of antibiotic-resistant bacteria in the absence of antibiotics has not been widely investigated. Here, we studied the morphologies of 10 antibiotic-resistant strains of <i>Escherichia coli</i> and used bioinformatics tools to classify the resistant cells under light microscopy in the absence of antibiotics. The antibiotic-resistant strains showed differences in morphology from the sensitive parental strain, and the differences were most prominent in the quinolone-and β-lactam-resistant bacteria. A cluster analysis revealed increased proportions of fatter or shorter cells in the antibiotic-resistant strains. A correlation analysis of morphological features and gene expression suggested that genes related to energy metabolism and antibiotic resistance were highly correlated with the morphological characteristics of the resistant strains. Our newly proposed deep learning method for single-cell classification achieved a high level of performance in classifying quinolone-and β-lactam-resistant strains.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11446759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-18DOI: 10.3389/fmicb.2024.1451582
Jing Mai, Ming-Jun Zhu, Bin-Bin Hu, Hong Zhang, Zhong-Hua Liu, Jian-Feng Sun, Yang Hu, Lu Zhao
IntroductionCarotenoids are important precursors of various aroma components in tobacco and play an important role in the sensory quality of tobacco. Phaffia rhodozyma is a species of Xanthophyllomyces capable of synthesizing a highly valuable carotenoid-astaxanthin, but has not yet been used in improving tobacco quality.MethodsThe dynamic changes of microbial community and metabolites during tobacco fermentation were analyzed in combination with microbiome and metabolome, and the quality of tobacco after fermentation was evaluated by sensory scores.ResultsP. rhodozyma could grow and produce carotenoids in tobacco extract, with a maximum biomass of 6.50 g/L and a maximum carotenoid production of 36.13 mg/L at 100 g/L tobacco extract. Meanwhile, the correlation analysis combined with microbiome and metabolomics showed that P. rhodozyma was significantly positively correlated with 11 metabolites such as 6-hydroxyluteolin and quercetin. Furthermore, the contents of alcohols, ketones and esters, which were important aromatic components in fermented tobacco, reached 77.57 μg/g, 58.28 μg/g and 73.51 μg/g, increasing 37.39%, 265.39% and 266.27% compared to the control group, respectively. Therefore, the aroma and flavor, and taste scores of fermented tobacco increased by 0.5 and 1.0 points respectively.DiscussionThis study confirmed that P. rhodozyma fermentation could effectively improve the sensory evaluation of tobacco, and provided a novel microbial fermentation method to improve tobacco quality.
{"title":"Effects of Phaffia rhodozyma on microbial community dynamics and tobacco quality during tobacco fermentation","authors":"Jing Mai, Ming-Jun Zhu, Bin-Bin Hu, Hong Zhang, Zhong-Hua Liu, Jian-Feng Sun, Yang Hu, Lu Zhao","doi":"10.3389/fmicb.2024.1451582","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1451582","url":null,"abstract":"IntroductionCarotenoids are important precursors of various aroma components in tobacco and play an important role in the sensory quality of tobacco. <jats:italic>Phaffia rhodozyma</jats:italic> is a species of <jats:italic>Xanthophyllomyces</jats:italic> capable of synthesizing a highly valuable carotenoid-astaxanthin, but has not yet been used in improving tobacco quality.MethodsThe dynamic changes of microbial community and metabolites during tobacco fermentation were analyzed in combination with microbiome and metabolome, and the quality of tobacco after fermentation was evaluated by sensory scores.Results<jats:italic>P. rhodozyma</jats:italic> could grow and produce carotenoids in tobacco extract, with a maximum biomass of 6.50 g/L and a maximum carotenoid production of 36.13 mg/L at 100 g/L tobacco extract. Meanwhile, the correlation analysis combined with microbiome and metabolomics showed that <jats:italic>P. rhodozyma</jats:italic> was significantly positively correlated with 11 metabolites such as 6-hydroxyluteolin and quercetin. Furthermore, the contents of alcohols, ketones and esters, which were important aromatic components in fermented tobacco, reached 77.57 μg/g, 58.28 μg/g and 73.51 μg/g, increasing 37.39%, 265.39% and 266.27% compared to the control group, respectively. Therefore, the aroma and flavor, and taste scores of fermented tobacco increased by 0.5 and 1.0 points respectively.DiscussionThis study confirmed that <jats:italic>P. rhodozyma</jats:italic> fermentation could effectively improve the sensory evaluation of tobacco, and provided a novel microbial fermentation method to improve tobacco quality.","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We evaluated the effects of cottonseed meal protein hydrolysate (CPH) on the intestinal microbiota of yellow-feather broilers. We randomly divided 240 chicks into four groups with six replicates: basal diet with 0% (CON), 1% (LCPH), 3% (MCPH), or 5% (HCPH) CPH. The test lasted 63 days and included days 1–21, 22–42, and 43–63 phases. The ACE, Chao1, and Shannon indices in the MCPH and HCPH groups of 42-day-old broilers were higher than those in the CON group (p < 0.05), indicating that the cecum microbial diversity and richness were higher in these groups. Firmicutes and Bacteroidetes were the dominant phyla; however, the main genera varied during the different periods. The abundance of Lactobacillus in CPH treatment groups of 21-day-old broilers was high (p < 0.05); in the 42-day-old broilers, the abundances of Barnesiella, Clostridia_vadinBB60_group, and Parasutterella in the LCPH group, Desulfovibrio, Lactobacillus, Clostridia_vadinBB60_group, and Butyricicoccus in the MCPH group, and Megamonas and Streptococcus in the HCPH group increased; in the 63-day-old broilers, the abundance of Clostridia_UCG-014 and Synergistes in the LCPH and HCPH group, respectively, increased (p < 0.05), and that of Alistipes in the LCPH and MCPH groups decreased (p < 0.05). And changes in the abundance of probiotics were beneficial to improve the intestinal morphology and growth performance. In addition, the LCPH treatment increased the complexity of the microbial network, while the MCPH treatment had the same effect in 42-day-old broilers. Thus, CPH increased the relative abundance of beneficial intestinal microbiota and enhanced the richness and diversity of the bacterial microbiota in broilers aged <42 days; this effect was weakened after 42 days.
{"title":"Effects of cottonseed meal protein hydrolysate on intestinal microbiota of yellow-feather broilers","authors":"Xiaoyang Zhang, Hailiang Wang, Yujie Niu, Cheng Chen, Wenju Zhang","doi":"10.3389/fmicb.2024.1434252","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1434252","url":null,"abstract":"We evaluated the effects of cottonseed meal protein hydrolysate (CPH) on the intestinal microbiota of yellow-feather broilers. We randomly divided 240 chicks into four groups with six replicates: basal diet with 0% (CON), 1% (LCPH), 3% (MCPH), or 5% (HCPH) CPH. The test lasted 63 days and included days 1–21, 22–42, and 43–63 phases. The ACE, Chao1, and Shannon indices in the MCPH and HCPH groups of 42-day-old broilers were higher than those in the CON group (<jats:italic>p</jats:italic> &lt; 0.05), indicating that the cecum microbial diversity and richness were higher in these groups. <jats:italic>Firmicutes</jats:italic> and <jats:italic>Bacteroidetes</jats:italic> were the dominant phyla; however, the main genera varied during the different periods. The abundance of <jats:italic>Lactobacillus</jats:italic> in CPH treatment groups of 21-day-old broilers was high (<jats:italic>p</jats:italic> &lt; 0.05); in the 42-day-old broilers, the abundances of <jats:italic>Barnesiella</jats:italic>, <jats:italic>Clostridia_vadinBB60_group</jats:italic>, and <jats:italic>Parasutterella</jats:italic> in the LCPH group, <jats:italic>Desulfovibrio</jats:italic>, <jats:italic>Lactobacillus</jats:italic>, <jats:italic>Clostridia_vadinBB60_group</jats:italic>, and <jats:italic>Butyricicoccus</jats:italic> in the MCPH group, and <jats:italic>Megamonas</jats:italic> and <jats:italic>Streptococcus</jats:italic> in the HCPH group increased; in the 63-day-old broilers, the abundance of <jats:italic>Clostridia_UCG-014</jats:italic> and <jats:italic>Synergistes</jats:italic> in the LCPH and HCPH group, respectively, increased (<jats:italic>p</jats:italic> &lt; 0.05), and that of <jats:italic>Alistipes</jats:italic> in the LCPH and MCPH groups decreased (<jats:italic>p</jats:italic> &lt; 0.05). And changes in the abundance of probiotics were beneficial to improve the intestinal morphology and growth performance. In addition, the LCPH treatment increased the complexity of the microbial network, while the MCPH treatment had the same effect in 42-day-old broilers. Thus, CPH increased the relative abundance of beneficial intestinal microbiota and enhanced the richness and diversity of the bacterial microbiota in broilers aged &lt;42 days; this effect was weakened after 42 days.","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-18DOI: 10.3389/fmicb.2024.1410820
Heather MacGregor, Isis Fukai, Kurt Ash, Adam Paul Arkin, Terry C. Hazen
As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as “characteristic communities of microorganisms” found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.
{"title":"Potential applications of microbial genomics in nuclear non-proliferation","authors":"Heather MacGregor, Isis Fukai, Kurt Ash, Adam Paul Arkin, Terry C. Hazen","doi":"10.3389/fmicb.2024.1410820","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1410820","url":null,"abstract":"As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as “characteristic communities of microorganisms” found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-18DOI: 10.3389/fmicb.2024.1433745
Mridula Chaturvedi, Navpreet Kaur, Pattanathu K. S. M. Rahman, Shashi Sharma
IntroductionEndocrine disrupting chemicals (EDCs) as benzene phenolic derivatives being hydrophobic partition to organic matter in sludge/soil sediments and show slow degradation rate owing to poor bioavailability to microbes.MethodsIn the present study, the potential of a versatile white rot fungal isolate S5 identified as Hypocrea lixii was monitored to degrade bisphenol A (BPA)/triclosan (TCS) under shake flask conditions with concomitant production of lipopeptide biosurfactant (BS) and plant growth promotion.ResultsSufficient growth of WRF for 5 days before supplementation of 50 ppm EDC (BPA/TCS) in set B showed an increase in degradation rates by 23% and 29% with corresponding increase in secretion of lignin-modifying enzymes compared to set A wherein almost 84% and 97% inhibition in fungal growth was observed when BPA/TCS were added at time of fungal inoculation. Further in set B, EDC concentration stimulated expression of laccase and lignin peroxidase (Lip) with 24.44 U/L of laccase and 281.69 U/L of Lip in 100 ppm BPA and 344 U/L Lip in 50 ppm TCS supplemented medium compared to their respective controls (without EDC). Biodegradation was also found to be correlated with lowering of surface tension from 57.02 mN/m (uninoculated control) to 44.16 mN/m in case of BPA and 38.49 mN/m in TCS, indicative of biosurfactant (BS) production. FTIR, GC-MS, and LC-ESI/MSMS confirmed the presence of surfactin lipopeptide isoforms. The WRF also displayed positive plant growth promoting traits as production of ammonia, indole acetic acid, siderophores, Zn solubilization, and 1-1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, reflecting its soil restoration ability.DiscussionThe combined traits of biosurfactant production, EDC degradation and plant growth promotion displayed by WRF will help in emulsifying the hydrophobic pollutants favoring their fast degradation along with restoration of contaminated soil in natural conditions.
{"title":"Solubilization and enhanced degradation of benzene phenolic derivatives—Bisphenol A/Triclosan using a biosurfactant producing white rot fungus Hypocrea lixii S5 with plant growth promoting traits","authors":"Mridula Chaturvedi, Navpreet Kaur, Pattanathu K. S. M. Rahman, Shashi Sharma","doi":"10.3389/fmicb.2024.1433745","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1433745","url":null,"abstract":"IntroductionEndocrine disrupting chemicals (EDCs) as benzene phenolic derivatives being hydrophobic partition to organic matter in sludge/soil sediments and show slow degradation rate owing to poor bioavailability to microbes.MethodsIn the present study, the potential of a versatile white rot fungal isolate S5 identified as <jats:italic>Hypocrea lixii</jats:italic> was monitored to degrade bisphenol A (BPA)/triclosan (TCS) under shake flask conditions with concomitant production of lipopeptide biosurfactant (BS) and plant growth promotion.ResultsSufficient growth of WRF for 5 days before supplementation of 50 ppm EDC (BPA/TCS) in set B showed an increase in degradation rates by 23% and 29% with corresponding increase in secretion of lignin-modifying enzymes compared to set A wherein almost 84% and 97% inhibition in fungal growth was observed when BPA/TCS were added at time of fungal inoculation. Further in set B, EDC concentration stimulated expression of laccase and lignin peroxidase (Lip) with 24.44 U/L of laccase and 281.69 U/L of Lip in 100 ppm BPA and 344 U/L Lip in 50 ppm TCS supplemented medium compared to their respective controls (without EDC). Biodegradation was also found to be correlated with lowering of surface tension from 57.02 mN/m (uninoculated control) to 44.16 mN/m in case of BPA and 38.49 mN/m in TCS, indicative of biosurfactant (BS) production. FTIR, GC-MS, and LC-ESI/MSMS confirmed the presence of surfactin lipopeptide isoforms. The WRF also displayed positive plant growth promoting traits as production of ammonia, indole acetic acid, siderophores, Zn solubilization, and 1-1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, reflecting its soil restoration ability.DiscussionThe combined traits of biosurfactant production, EDC degradation and plant growth promotion displayed by WRF will help in emulsifying the hydrophobic pollutants favoring their fast degradation along with restoration of contaminated soil in natural conditions.","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-18DOI: 10.3389/fmicb.2024.1439814
Jahn Nitschke, Robin Huber, Stefania Vossio, Dimitri Moreau, Laurence Marcourt, Katia Gindro, Emerson F. Queiroz, Thierry Soldati, Nabil Hanna
IntroductionMycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, remains a serious threat to human health worldwide and the quest for new anti-tubercular drugs is an enduring and demanding journey. Natural products (NPs) have played a significant role in advancing drug therapy of infectious diseases.MethodsThis study evaluated the suitability of a high-throughput infection system composed of the host amoeba Dictyostelium discoideum (Dd) and Mycobacterium marinum (Mm), a close relative of Mtb, to identify anti-infective compounds. Growth of Dd and intracellular Mm were quantified by using luminescence and fluorescence readouts in phenotypic assays. The system was first benchmarked with a set of therapeutic anti-Mtb antibiotics and then used to screen a library of biotransformed stilbenes.ResultsThe study confirmed both efficacy of established antibiotics such as rifampicin and bedaquiline, with activities below defined anti-mycobacterium susceptibility breakpoints, and the lack of activity of pyrazinamide against Mm. The screening revealed the promising anti-infective activities of trans-δ-viniferins and in particular of two compounds 17 and 19 with an IC50 of 18.1 μM, 9 μM, respectively. Both compounds had no activity on Mm in broth. Subsequent exploration via halogenation and structure-activity relationship studies led to the identification of derivatives with improved selectivity and potency. The modes of action of the anti-infective compounds may involve inhibition of mycobacterial virulence factors or boosting of host defense.DiscussionThe study highlights the potential of biotransformation and NP-inspired derivatization approaches for drug discovery and underscores the utility of the Dd-Mm infection system in identifying novel anti-infective compounds.
引言 结核分枝杆菌(Mtb)是结核病的致病菌,它仍然严重威胁着全世界人类的健康,寻找新的抗结核药物是一项艰巨而持久的任务。本研究评估了由宿主变形虫盘基变形虫(Dd)和Mtb的近亲海洋分枝杆菌(Mm)组成的高通量感染系统在鉴定抗感染化合物方面的适用性。在表型测定中使用发光和荧光读数对 Dd 和细胞内 Mm 的生长进行量化。该系统首先以一组治疗性抗 Mtb 抗生素为基准,然后用于筛选生物转化二苯乙烯类化合物库。结果该研究证实了利福平和贝达喹啉等既有抗生素的有效性(其活性低于规定的抗分枝杆菌药敏断点),以及吡嗪酰胺对 Mm 缺乏活性。筛选结果表明,反式-δ-维尼芬类化合物具有良好的抗感染活性,尤其是 17 和 19 这两个化合物,其 IC50 分别为 18.1 μM 和 9 μM。这两种化合物对肉汤中的 Mm 没有活性。随后,通过卤化和结构-活性关系研究,发现了具有更好选择性和效力的衍生物。该研究强调了生物转化和 NP 启发的衍生化方法在药物发现方面的潜力,并强调了 Dd-Mm 感染系统在鉴定新型抗感染化合物方面的实用性。
{"title":"Discovery of anti-infective compounds against Mycobacterium marinum after biotransformation of simple natural stilbenes by a fungal secretome","authors":"Jahn Nitschke, Robin Huber, Stefania Vossio, Dimitri Moreau, Laurence Marcourt, Katia Gindro, Emerson F. Queiroz, Thierry Soldati, Nabil Hanna","doi":"10.3389/fmicb.2024.1439814","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1439814","url":null,"abstract":"Introduction<jats:italic>Mycobacterium tuberculosis</jats:italic> (Mtb), the causative agent of tuberculosis, remains a serious threat to human health worldwide and the quest for new anti-tubercular drugs is an enduring and demanding journey. Natural products (NPs) have played a significant role in advancing drug therapy of infectious diseases.MethodsThis study evaluated the suitability of a high-throughput infection system composed of the host amoeba <jats:italic>Dictyostelium discoideum</jats:italic> (Dd) and <jats:italic>Mycobacterium marinum</jats:italic> (Mm), a close relative of Mtb, to identify anti-infective compounds. Growth of Dd and intracellular Mm were quantified by using luminescence and fluorescence readouts in phenotypic assays. The system was first benchmarked with a set of therapeutic anti-Mtb antibiotics and then used to screen a library of biotransformed stilbenes.ResultsThe study confirmed both efficacy of established antibiotics such as rifampicin and bedaquiline, with activities below defined anti-mycobacterium susceptibility breakpoints, and the lack of activity of pyrazinamide against Mm. The screening revealed the promising anti-infective activities of <jats:italic>trans</jats:italic>-δ-viniferins and in particular of two compounds 17 and 19 with an IC<jats:sub>50</jats:sub> of 18.1 μM, 9 μM, respectively. Both compounds had no activity on Mm in broth. Subsequent exploration via halogenation and structure-activity relationship studies led to the identification of derivatives with improved selectivity and potency. The modes of action of the anti-infective compounds may involve inhibition of mycobacterial virulence factors or boosting of host defense.DiscussionThe study highlights the potential of biotransformation and NP-inspired derivatization approaches for drug discovery and underscores the utility of the Dd-Mm infection system in identifying novel anti-infective compounds.","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-18DOI: 10.3389/fmicb.2024.1439532
Kuang-Hung Liu, Yu-Xin Xiao, Ruwen Jou
IntroductionMultidrug-resistant tuberculosis (MDR-TB) remains a challenge in the TB program of Taiwan, where 0.5% of new cases and 2.1% of previously treated cases were resistant to at least rifampin (RIF) and isoniazid (INH). Since >80% of our MDR-TB are new cases, genotyping of MDR Mycobacterium tuberculosis is implemented to facilitate contact investigation, cluster identification, and outbreak delineation.MethodsThis is a population-based retrospective cohort study analyzing MDR-TB cases from 2019 to 2022. Whole genome sequencing (WGS) was performed using the Illumina MiSeq and analyzed using the TB Profiler. A single nucleotide polymorphism (SNP) threshold of ≤ 12 and phylogenetic methods were used to identify putative transmission clusters. An outbreak was confirmed using genomic data and epidemiologic links.ResultsOf the 297 MDR-TB cases, 246 (82.8%), 45 (15.2%), and 6 (2.0%) were simple MDR, extensively drug-resistant tuberculosis (pre-XDR-TB) and extensively drug-resistant tuberculosis (XDR-TB), respectively. The sublineage 2.2 modern Beijing was the predominant (48.8%) MDR-TB strain in Taiwan. Phylogenetic analysis identified 25.3% isolates in 20 clusters, with cluster sizes ranging from 2 to 13 isolates. Nevertheless, only 2 clusters, one household and one community, were confirmed as outbreaks. In this study, we found that males had a higher risk of MDR-TB transmission compared to females, and those infected with the sublineage 2.1-proto-Beijing genotype isolates were at a higher risk of transmission. Furthermore, 161 (54.2%) isolates harbored compensatory mutations in the rpoC and non-rifampicin resistant determinant region (non-RRDR) of the rpoB gene. MDR-TB strains containing rpoB S450L and other compensatory mutations concurrently were significantly associated with clusters, especially the proto-Beijing genotype strains with the compensatory mutation rpoC E750D or the modern Beijing genotype strains with rpoC D485Y/rpoC E1140D.DiscussionRoutine and continuous surveillance using WGS-based analysis is recommended to warn of risks and delineate transmission clusters of MDR-TB. We proposed the use of compensatory mutations as epidemiological markers of M. tuberculosis to interrupt putative MDR-TB transmission.
{"title":"Multidrug-resistant tuberculosis clusters and transmission in Taiwan: a population-based cohort study","authors":"Kuang-Hung Liu, Yu-Xin Xiao, Ruwen Jou","doi":"10.3389/fmicb.2024.1439532","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1439532","url":null,"abstract":"IntroductionMultidrug-resistant tuberculosis (MDR-TB) remains a challenge in the TB program of Taiwan, where 0.5% of new cases and 2.1% of previously treated cases were resistant to at least rifampin (RIF) and isoniazid (INH). Since &gt;80% of our MDR-TB are new cases, genotyping of MDR <jats:italic>Mycobacterium tuberculosis</jats:italic> is implemented to facilitate contact investigation, cluster identification, and outbreak delineation.MethodsThis is a population-based retrospective cohort study analyzing MDR-TB cases from 2019 to 2022. Whole genome sequencing (WGS) was performed using the Illumina MiSeq and analyzed using the TB Profiler. A single nucleotide polymorphism (SNP) threshold of ≤ 12 and phylogenetic methods were used to identify putative transmission clusters. An outbreak was confirmed using genomic data and epidemiologic links.ResultsOf the 297 MDR-TB cases, 246 (82.8%), 45 (15.2%), and 6 (2.0%) were simple MDR, extensively drug-resistant tuberculosis (pre-XDR-TB) and extensively drug-resistant tuberculosis (XDR-TB), respectively. The sublineage 2.2 modern Beijing was the predominant (48.8%) MDR-TB strain in Taiwan. Phylogenetic analysis identified 25.3% isolates in 20 clusters, with cluster sizes ranging from 2 to 13 isolates. Nevertheless, only 2 clusters, one household and one community, were confirmed as outbreaks. In this study, we found that males had a higher risk of MDR-TB transmission compared to females, and those infected with the sublineage 2.1-proto-Beijing genotype isolates were at a higher risk of transmission. Furthermore, 161 (54.2%) isolates harbored compensatory mutations in the <jats:italic>rpoC</jats:italic> and non-rifampicin resistant determinant region (non-RRDR) of the rpoB gene. MDR-TB strains containing rpoB S450L and other compensatory mutations concurrently were significantly associated with clusters, especially the proto-Beijing genotype strains with the compensatory mutation <jats:italic>rpoC</jats:italic> E750D or the modern Beijing genotype strains with <jats:italic>rpoC</jats:italic> D485Y/<jats:italic>rpoC</jats:italic> E1140D.DiscussionRoutine and continuous surveillance using WGS-based analysis is recommended to warn of risks and delineate transmission clusters of MDR-TB. We proposed the use of compensatory mutations as epidemiological markers of M. tuberculosis to interrupt putative MDR-TB transmission.","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bacteriophages are the most prolific organisms on Earth, yet many of their genomes and assemblies from metagenomic sources lack protein sequences with identified functions. While most bacteriophage proteins are structural proteins, categorized as Phage Virion Proteins (PVPs), a considerable number remain unclassified. Complicating matters further, traditional lab-based methods for PVP identification can be tedious. To expedite the process of identifying PVPs, machine-learning models are increasingly being employed. Existing tools have developed models for predicting PVPs from protein sequences as input. However, none of these efforts have built software allowing for both genomic and metagenomic data as input. In addition, there is currently no framework available for easily curating data and creating new types of machine learning models. In response, we introduce PhageScanner, an open-source platform that streamlines data collection for genomic and metagenomic datasets, model training and testing, and includes a prediction pipeline for annotating genomic and metagenomic data. PhageScanner also features a graphical user interface (GUI) for visualizing annotations on genomic and metagenomic data. We further introduce a BLAST-based classifier that outperforms ML-based models and an efficient Long Short-Term Memory (LSTM) classifier. We then showcase the capabilities of PhageScanner by predicting PVPs in six previously uncharacterized bacteriophage genomes. In addition, we create a new model that predicts phage-encoded toxins within bacteriophage genomes, thus displaying the utility of the framework.
{"title":"PhageScanner: a reconfigurable machine learning framework for bacteriophage genomic and metagenomic feature annotation","authors":"Dreycey Albin, Michelle Ramsahoye, Eitan Kochavi, Mirela Alistar","doi":"10.3389/fmicb.2024.1446097","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1446097","url":null,"abstract":"Bacteriophages are the most prolific organisms on Earth, yet many of their genomes and assemblies from metagenomic sources lack protein sequences with identified functions. While most bacteriophage proteins are structural proteins, categorized as Phage Virion Proteins (PVPs), a considerable number remain unclassified. Complicating matters further, traditional lab-based methods for PVP identification can be tedious. To expedite the process of identifying PVPs, machine-learning models are increasingly being employed. Existing tools have developed models for predicting PVPs from protein sequences as input. However, none of these efforts have built software allowing for both genomic and metagenomic data as input. In addition, there is currently no framework available for easily curating data and creating new types of machine learning models. In response, we introduce PhageScanner, an open-source platform that streamlines data collection for genomic and metagenomic datasets, model training and testing, and includes a prediction pipeline for annotating genomic and metagenomic data. PhageScanner also features a graphical user interface (GUI) for visualizing annotations on genomic and metagenomic data. We further introduce a BLAST-based classifier that outperforms ML-based models and an efficient Long Short-Term Memory (LSTM) classifier. We then showcase the capabilities of PhageScanner by predicting PVPs in six previously uncharacterized bacteriophage genomes. In addition, we create a new model that predicts phage-encoded toxins within bacteriophage genomes, thus displaying the utility of the framework.","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}