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Can a microbial community become an evolutionary individual? 微生物群落能成为一个进化的个体吗？
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-20 DOI: 10.1016/j.mib.2025.102596
Afra Salazar , Sara Mitri
{"title":"Can a microbial community become an evolutionary individual?","authors":"Afra Salazar ,&nbsp;Sara Mitri","doi":"10.1016/j.mib.2025.102596","DOIUrl":"10.1016/j.mib.2025.102596","url":null,"abstract":"<div><div>Microbial communities provide crucial services for human well-being, driving an interest in designing and controlling them towards optimised or novel functions. Unfortunately, promising strategies such as community breeding — sometimes referred to as ‘directed evolution’ or ‘artificial community selection’ — have shown limited success. A key issue is that microbial communities do not reliably exhibit heritable variation, limiting their capacity for adaptive evolution. In other words, microbial communities are not evolutionary individuals. Here, we provide an overview of the literature on evolutionary transitions in individuality and, with insights from paradigmatic organisms, build a multidimensional space in which the individuality of a multispecies community is characterised by three ecological traits: positive interactions, functional integration, and entrenchment. We then place microbial communities within this individuality space, explore how they can be directed toward increased individuality, and discuss how this perspective can help improve our approach to community breeding.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"84 ","pages":"Article 102596"},"PeriodicalIF":5.9,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143444717","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}
引用次数: 0
Targeted isolation of piperazate-containing molecules: bioinformatics and spectroscopy 含哌酸酯分子的靶向分离：生物信息学和光谱学
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-16 DOI: 10.1016/j.mib.2025.102584
Mostafa Hagar , Sangwook Kang , Raymond J Andersen , Dong-Chan Oh , Katherine S Ryan
{"title":"Targeted isolation of piperazate-containing molecules: bioinformatics and spectroscopy","authors":"Mostafa Hagar ,&nbsp;Sangwook Kang ,&nbsp;Raymond J Andersen ,&nbsp;Dong-Chan Oh ,&nbsp;Katherine S Ryan","doi":"10.1016/j.mib.2025.102584","DOIUrl":"10.1016/j.mib.2025.102584","url":null,"abstract":"<div><div>Piperazic acid (Piz) is an intriguing hydrazine-containing amino acid found in a diverse variety of natural products, the majority of which are bioactive. Recently, several approaches have been reported for targeted isolation of Piz-containing molecules, combining spectroscopic techniques for screening Piz moieties with recent advances in Piz biosynthesis. Here, we highlight bioactive natural products recently isolated using these methods and bring into focus structural elucidation challenges impeding the discovery of more Piz-containing molecules.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"84 ","pages":"Article 102584"},"PeriodicalIF":5.9,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143419854","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}
引用次数: 0
Protein families secreted by nematodes to modulate host immunity 线虫分泌调节宿主免疫的蛋白家族
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-15 DOI: 10.1016/j.mib.2025.102582
Florent Colomb, Henry J McSorley
{"title":"Protein families secreted by nematodes to modulate host immunity","authors":"Florent Colomb,&nbsp;Henry J McSorley","doi":"10.1016/j.mib.2025.102582","DOIUrl":"10.1016/j.mib.2025.102582","url":null,"abstract":"<div><div>Parasitic nematodes release a wide variety of immunomodulatory proteins, which allow them to escape the host’s immune-mediated killing or ejection mechanisms. This immunomodulation is mediated by nematode excretory/secretory (E/S) products, which contain multiple families of immunomodulatory proteins. Many of these families are conserved across different parasitic nematodes, while others are apparently unique to specific species. While some E/S products interact with host proteins, others have evolved to target host lipids, glycans, and metabolites. In this review, we will focus on three families of immunomodulatory proteins, which are particularly expanded in intestinal nematodes: the venom allergen-like proteins, the apyrases, and the complement control protein domain-containing proteins. These families of proteins suppress host immune responses, and evidence is gathering that these could be effective vaccine antigens against these intractable parasites.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"84 ","pages":"Article 102582"},"PeriodicalIF":5.9,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143419852","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}
引用次数: 0
A CRISPR view on genetic screens in Toxoplasma gondii 刚地弓形虫基因筛选的CRISPR观点。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2024.102577
Franziska Hildebrandt , Ana N. Matias , Moritz Treeck
{"title":"A CRISPR view on genetic screens in Toxoplasma gondii","authors":"Franziska Hildebrandt ,&nbsp;Ana N. Matias ,&nbsp;Moritz Treeck","doi":"10.1016/j.mib.2024.102577","DOIUrl":"10.1016/j.mib.2024.102577","url":null,"abstract":"<div><div>Genome editing technologies, such as CRISPR-Cas9, have revolutionised the study of genes in a variety of organisms, including unicellular parasites. Today, the CRISPR-Cas9 technology is vastly applied in high-throughput screens to investigate interactions between the Apicomplexan parasite <em>Toxoplasma gondii</em> and its hosts. <em>In vitro</em> and <em>in vivo T. gondii</em> screens performed in naive and restrictive conditions have led to the discovery of essential and fitness-conferring <em>T. gondii</em> genes, as well as factors important for virulence and dissemination. Recent studies have adapted the CRISPR-Cas9 screening technology to study <em>T. gondii</em> genes based on phenotypes unrelated to parasite survival. These advances were achieved by using conditional systems coupled with imaging, as well as single-cell RNA sequencing and phenotypic selection. Here, we review the state-of-the-art of CRISPR-Cas9 screening technologies with a focus on <em>T. gondii</em>, highlighting strengths, current limitations and future avenues for its development, including its application to other Apicomplexan species.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102577"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142946126","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}
引用次数: 0
Gram-positive pathogens, inflammation, and the host lipid environment 革兰氏阳性病原体，炎症和宿主脂质环境
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2025.102581
Reginald A Woods , Sarai Guzman Vela , Francis Alonzo III
{"title":"Gram-positive pathogens, inflammation, and the host lipid environment","authors":"Reginald A Woods ,&nbsp;Sarai Guzman Vela ,&nbsp;Francis Alonzo III","doi":"10.1016/j.mib.2025.102581","DOIUrl":"10.1016/j.mib.2025.102581","url":null,"abstract":"<div><div>The host lipid environment is a barrier to bacterial infection that comprises antimicrobial fatty acids and impermeable lipids that keep infectious agents from penetrating tissues. Bacterial and host lipids also signal to the immune system to regulate inflammation. Notably, bacterial lipids activate Toll-like receptors to initiate cytokine production, immune cell recruitment, and oxidative burst to control infection. Bacterial pathogens must adapt to the lipid environment, including bactericidal host fatty acids and inflammatory lipids, in ways that promote persistence in diverse tissues. Here, we discuss current advances in the understanding of <em>Staphylococcus aureus</em> lipid interactions that contribute to inflammation and innate immunity and consider the complex roles of host inflammatory lipids in driving immune defenses and antibacterial activity. In addition, we endeavor to introduce similar processes in other Gram-positive pathogens. These recent studies highlight the growing body of knowledge on the effects of lipid metabolism on host immunity and pathogenesis.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102581"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143360567","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}
引用次数: 0
Harnessing gut microbial communities to unravel microbiome functions 利用肠道微生物群落来揭示微生物群的功能。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2024.102578
Samir Giri , Handuo Shi , Athanasios Typas , Kerwyn Casey Huang
{"title":"Harnessing gut microbial communities to unravel microbiome functions","authors":"Samir Giri ,&nbsp;Handuo Shi ,&nbsp;Athanasios Typas ,&nbsp;Kerwyn Casey Huang","doi":"10.1016/j.mib.2024.102578","DOIUrl":"10.1016/j.mib.2024.102578","url":null,"abstract":"<div><div>The gut microbiome impacts human health in direct and indirect ways. While many associations have been discovered between specific microbiome compositions and diseases, establishing causality, understanding the underlying mechanisms, and developing successful microbiome-based therapies require novel experimental approaches. In this opinion, we discuss how <em>in vitro</em> cultivation of diverse communities enables systematic investigation of the individual and collective functions of gut microbes. Up to now, the field has relied mostly on simple, bottom-up assembled synthetic communities or more complex, undefined stool-derived communities. Although powerful for dissecting interactions and mapping causal effects, these communities suffer either from ignoring the complexity, diversity, coevolution, and dynamics of natural communities or from lack of control of community composition. These limitations can be overcome in the future by establishing personalized culture collections from stool samples of different donors and assembling personalized communities to investigate native interactions and ecological relationships in a controlled manner.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102578"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142946135","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}
引用次数: 0
The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes 微生物组设计的理论与数据架构：迈向微生物组的s矩阵。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2025.102580
Shreya Arya , Ashish B George , James O'Dwyer
{"title":"The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes","authors":"Shreya Arya ,&nbsp;Ashish B George ,&nbsp;James O'Dwyer","doi":"10.1016/j.mib.2025.102580","DOIUrl":"10.1016/j.mib.2025.102580","url":null,"abstract":"<div><div>Designing microbiomes for applications in health, bioengineering, and sustainability is intrinsically linked to a fundamental theoretical understanding of the rules governing microbial community assembly. Microbial ecologists have used a range of mathematical models to understand, predict, and control microbiomes, ranging from mechanistic models, putting microbial populations and their interactions as the focus, to purely statistical approaches, searching for patterns in empirical and experimental data. We review the success and limitations of these modeling approaches when designing novel microbiomes, especially when guided by (inevitably) incomplete experimental data. Although successful at predicting generic patterns of community assembly, mechanistic and phenomenological models tend to fall short of the precision needed to design and implement specific functionality in a microbiome. We argue that to effectively design microbiomes with optimal functions in diverse environments, ecologists should combine data-driven techniques with mechanistic models — a middle, third way for using theory to inform design.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102580"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028176","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}
引用次数: 0
Alginate catabolic systems in marine bacteria 海藻酸盐在海洋细菌中的分解代谢系统。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2024.102564
Fei Xu , Xiu-Lan Chen , Yu-Zhong Zhang
{"title":"Alginate catabolic systems in marine bacteria","authors":"Fei Xu ,&nbsp;Xiu-Lan Chen ,&nbsp;Yu-Zhong Zhang","doi":"10.1016/j.mib.2024.102564","DOIUrl":"10.1016/j.mib.2024.102564","url":null,"abstract":"<div><div>Brown algae, constituting the second largest group of marine macroalgae, fix significant amounts of inorganic carbon into alginate, the most abundant polysaccharide found in their cell walls. Alginate serves as an important macromolecular carbon source for marine bacteria. The catabolism of alginate by bacteria is an important step in the marine carbon cycle, and this area of research has attracted growing interests over the past decade. Here, we provide an overview of the recent advances in our understanding of marine bacterial alginate catabolic systems, both in individual organisms and within bacterial consortia, discuss the possibility of additional alginate metabolic pathways in light of the present findings, and highlight the future research foci.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102564"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806441","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}
引用次数: 0
Revisiting the potential of natural products in antimycobacterial therapy: advances in drug discovery and semisynthetic solutions 重新审视天然产物在抗细菌治疗中的潜力：药物发现和半合成解决方案的进展。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2024.102576
Maya George, Gerard D Wright
{"title":"Revisiting the potential of natural products in antimycobacterial therapy: advances in drug discovery and semisynthetic solutions","authors":"Maya George,&nbsp;Gerard D Wright","doi":"10.1016/j.mib.2024.102576","DOIUrl":"10.1016/j.mib.2024.102576","url":null,"abstract":"<div><div>Natural products have been pivotal in treating mycobacterial infections with early antibiotics such as streptomycin, forming the foundation of tuberculosis therapy. However, the emergence of multidrug-resistant and extensively drug-resistant <em>Mycobacterium</em> species has intensified the need for novel antimycobacterial agents. In this review, we revisit the historical contributions of natural products to antimycobacterial drug discovery and highlight recent advances in the field. We assess the application of molecular networking and the exploration of unculturable bacteria in identifying new antimycobacterial compounds such as amycobactin and levesquamides. We also highlight the role of semisynthesis in optimizing natural products, exemplified by sequanamycins and spectinomycin analogs that evade <em>M. tuberculosis’</em> intrinsic resistance. Finally, we discuss emerging technologies that are promising to accelerate the discovery and development of next-generation antimycobacterial therapies. Despite ongoing challenges, these innovative approaches offer renewed hope in addressing the growing crisis of drug-resistant mycobacterial infections.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102576"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913930","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}
引用次数: 0
The promise of CRISPR-associated transposons for bacterial functional genomics crispr相关转座子在细菌功能基因组学中的应用前景。
IF 5.9 2区 生物学
Current opinion in microbiology Pub Date : 2025-02-01 DOI: 10.1016/j.mib.2024.102563
Amy B Banta , Rodrigo A Cuellar , Nischala Nadig , Bryce C Davis , Jason M Peters
{"title":"The promise of CRISPR-associated transposons for bacterial functional genomics","authors":"Amy B Banta ,&nbsp;Rodrigo A Cuellar ,&nbsp;Nischala Nadig ,&nbsp;Bryce C Davis ,&nbsp;Jason M Peters","doi":"10.1016/j.mib.2024.102563","DOIUrl":"10.1016/j.mib.2024.102563","url":null,"abstract":"<div><div>CRISPR-associated transposons (CASTs) are naturally occurring amalgamations of CRISPR-Cas machinery and Tn<em>7</em>-like transposons that direct site-specific integration of transposon DNA via programmable guide RNAs. Although the mechanisms of CAST-based transposition have been well studied at the molecular and structural level, CASTs have yet to be broadly applied to bacterial genome engineering and systematic gene phenotyping (i.e. functional genomics) — likely due to their relatively recent discovery. Here, we describe the function and applications of CASTs, focusing on well-characterized systems, including the type I-F CAST from <em>Vibrio cholerae</em> (VcCAST) and type V-K CAST from <em>Scytonema hofmanni</em> (ShCAST). Further, we discuss the potentially transformative impact of targeted transposition on bacterial functional genomics by proposing genome-scale extensions of existing CAST tools.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"Article 102563"},"PeriodicalIF":5.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779649","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}
引用次数: 0
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