Pub Date : 2025-01-01Epub Date: 2025-01-22DOI: 10.1016/j.crmicr.2025.100347
Yi-Ni Ma , Xun Xu , Lai-Feng Chen , Jin-Ping Zhou , Zhen-Hui Cao , Qiu-Ye Lin
The present study aimed to optimize the processing technology of natto fermented with Bacillus subtilis natto and Limosilactobacillus fermentum 2–2 and its effect on quality characteristics as well as volatile compounds. The results of single-factor tests and response surface methodology (RSM) showed that the optimal fermentation conditions of natto were L. fermentum inoculation amount of 0.3 %, fermentation temperature at 39 °C, fermentation time of 48 h, and after-ripening time of 24 h. Compared with natto control with B. subtilis natto only, natto co-cultured with B. subtilis natto and L. fermentum 2–2 showed higher scavenging ability of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and greater nattokinase activity. Volatomics analysis revealed that 71 differential volatile compounds were identified with 23 up-regulated and 48 down-regulated. Especially, co-fermentation of B. subtilis natto and L. fermentum 2–2 increased generation of alcohols, ketones and esters while reduced pyrazines formation. The above results indicate that co-culture of B. subtilis natto and L. fermentum can enhance the antioxidant and nattokinase activity and modify the volatile profile in natto and have the potential for application as the mixed starter in natto production.
{"title":"Process optimization and evaluation of quality properties of natto with co-culture of Bacillus subtilis natto and Limosilactobacillus fermentum","authors":"Yi-Ni Ma , Xun Xu , Lai-Feng Chen , Jin-Ping Zhou , Zhen-Hui Cao , Qiu-Ye Lin","doi":"10.1016/j.crmicr.2025.100347","DOIUrl":"10.1016/j.crmicr.2025.100347","url":null,"abstract":"<div><div>The present study aimed to optimize the processing technology of natto fermented with <em>Bacillus subtilis</em> natto and <em>Limosilactobacillus fermentum</em> 2–2 and its effect on quality characteristics as well as volatile compounds. The results of single-factor tests and response surface methodology (RSM) showed that the optimal fermentation conditions of natto were L. <em>fermentum</em> inoculation amount of 0.3 %, fermentation temperature at 39 °C, fermentation time of 48 h, and after-ripening time of 24 h. Compared with natto control with <em>B. subtilis</em> natto only, natto co-cultured with <em>B. subtilis</em> natto and L. <em>fermentum</em> 2–2 showed higher scavenging ability of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and greater nattokinase activity. Volatomics analysis revealed that 71 differential volatile compounds were identified with 23 up-regulated and 48 down-regulated. Especially, co-fermentation of <em>B. subtilis</em> natto and L. <em>fermentum</em> 2–2 increased generation of alcohols, ketones and esters while reduced pyrazines formation. The above results indicate that co-culture of <em>B. subtilis</em> natto and L. <em>fermentum</em> can enhance the antioxidant and nattokinase activity and modify the volatile profile in natto and have the potential for application as the mixed starter in natto production.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100347"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143105056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mangrovibacter phragmitis is a Gram-negative bacterium typically found in plant roots that supports nitrogen fixation in nutrient-poor environments such as mangrove ecosystems. Although primarily found in environmental niches, an unusual case in Thailand of M. phragmitis strain PSU-3885–11 isolated from the sputum of a 29-year-old female patient with spinal tuberculosis. This isolate was initially misidentified as part of the Enterobacter cloacae complex (ECC) by MALDI-TOF. However, WGS subsequently confirmed its correct identity as M. phragmitis. The genome contains 4,651 coding sequences, along with 72 tRNA genes and 1 tmRNA. Moreover, comparative genomic analysis showed 99.32 % average nucleotide identity (ANI) similar to M. phragmitis MP23, and several antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were identified in the PSU-3885–11 genome which may contribute to its ability to survive in diverse environments, including human hosts. The PSU-3885–11 displayed resistance to beta-lactam antibiotics such as ampicillin and cefotaxime, while remaining sensitive to a wide range of other antibiotics. Key virulence genes including ompA, hcp/tssD, and rpoS, were identified which may play a role in its persistence in human hosts as an opportunistic pathogen. The presence of ribosomally synthesized and post-translationally modified peptides (RiPPs) and bacteriocins indicates the antimicrobial properties that may provide a competitive advantage in both environmental and clinical settings of this strain. Therefore, this study provides valuable insights into the genomic features, antibiotic resistance, and potential pathogenicity of M. phragmitis PSU-3885–11. The findings also emphasize the importance of continued surveillance and genomic analysis of environmental bacteria that may emerge as opportunistic pathogens in human infections.
{"title":"First whole genome report of Mangrovibacter phragmitis PSU-3885–11 isolated from a patient in Thailand","authors":"Nattarika Chaichana , Thunchanok Yaikhan , Mingkwan Yingkajorn , Nonthawat Thepsimanon , Sirikan Suwannasin , Kamonnut Singkhamanan , Sarunyou Chusri , Rattanaruji Pomwised , Monwadee Wonglapsuwan , Komwit Surachat","doi":"10.1016/j.crmicr.2025.100350","DOIUrl":"10.1016/j.crmicr.2025.100350","url":null,"abstract":"<div><div><em>Mangrovibacter phragmitis</em> is a Gram-negative bacterium typically found in plant roots that supports nitrogen fixation in nutrient-poor environments such as mangrove ecosystems. Although primarily found in environmental niches, an unusual case in Thailand of <em>M. phragmitis</em> strain PSU-3885–11 isolated from the sputum of a 29-year-old female patient with spinal tuberculosis. This isolate was initially misidentified as part of the <em>Enterobacter cloacae</em> complex (ECC) by MALDI-TOF. However, WGS subsequently confirmed its correct identity as <em>M. phragmitis</em>. The genome contains 4,651 coding sequences, along with 72 tRNA genes and 1 tmRNA. Moreover, comparative genomic analysis showed 99.32 % average nucleotide identity (ANI) similar to <em>M. phragmitis</em> MP23, and several antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were identified in the PSU-3885–11 genome which may contribute to its ability to survive in diverse environments, including human hosts. The PSU-3885–11 displayed resistance to beta-lactam antibiotics such as ampicillin and cefotaxime, while remaining sensitive to a wide range of other antibiotics. Key virulence genes including <em>ompA, hcp/tssD,</em> and <em>rpoS</em>, were identified which may play a role in its persistence in human hosts as an opportunistic pathogen. The presence of ribosomally synthesized and post-translationally modified peptides (RiPPs) and bacteriocins indicates the antimicrobial properties that may provide a competitive advantage in both environmental and clinical settings of this strain. Therefore, this study provides valuable insights into the genomic features, antibiotic resistance, and potential pathogenicity of <em>M. phragmitis</em> PSU-3885–11. The findings also emphasize the importance of continued surveillance and genomic analysis of environmental bacteria that may emerge as opportunistic pathogens in human infections.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100350"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143105139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01Epub Date: 2025-05-12DOI: 10.1016/j.crmicr.2025.100404
Pengfei Niu , Rong Guo , Chan Ding , Shengqing Yu
The type IX secretion system (T9SS) is specific to the Fibrobacteres-Chlorobi-Bacteroidetes superphylum, the members of which have many specialized features, including gliding motility and the transport of cargo proteins across the outer membrane. At least 20 proteins have been identified as the components of T9SS. Proteins secreted by T9SS use the Sec system to cross the inner membrane, and the conserved C-terminal domain targets them to the T9SS for delivery to the extracellular environment or attachment to the outer membrane. Riemerella anatipestifer is an important pathogen of waterfowl, causing septicemic and exudative diseases. A genetic analysis recently detected T9SS in R. anatipestifer, in which it transports proteins and affects virulence. Moreover, at least 19 T9SS-transported proteins in R. anatipestifer strain Yb2 were identified, with multiple functions and affecting R. anatipestifer in different ways. In this review, we focus on recent advances in our understanding of the structure, function, and organization of the T9SS machinery and new findings about this highly novel secretion system in R. anatipestifer.
{"title":"Advances in the type IX secretion system: an exploration focusing on Riemerella anatipestifer","authors":"Pengfei Niu , Rong Guo , Chan Ding , Shengqing Yu","doi":"10.1016/j.crmicr.2025.100404","DOIUrl":"10.1016/j.crmicr.2025.100404","url":null,"abstract":"<div><div>The type IX secretion system (T9SS) is specific to the Fibrobacteres-Chlorobi-Bacteroidetes superphylum, the members of which have many specialized features, including gliding motility and the transport of cargo proteins across the outer membrane. At least 20 proteins have been identified as the components of T9SS. Proteins secreted by T9SS use the Sec system to cross the inner membrane, and the conserved C-terminal domain targets them to the T9SS for delivery to the extracellular environment or attachment to the outer membrane. <em>Riemerella anatipestifer</em> is an important pathogen of waterfowl, causing septicemic and exudative diseases. A genetic analysis recently detected T9SS in <em>R. anatipestifer</em>, in which it transports proteins and affects virulence. Moreover, at least 19 T9SS-transported proteins in <em>R. anatipestifer</em> strain Yb2 were identified, with multiple functions and affecting <em>R. anatipestifer</em> in different ways. In this review, we focus on recent advances in our understanding of the structure, function, and organization of the T9SS machinery and new findings about this highly novel secretion system in <em>R. anatipestifer</em>.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100404"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144893496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Prostate cancer (PCa) is a major cause of cancer-related deaths worldwide. While current treatments such as surveillance, surgery, and radiation are effective, they have their limitations. These can include patient incompliance due to side effects or resistance to hormonal changes, highlighting the need for alternative approaches. Human microbiota, a complex and dynamic host, plays a significant role in the homeostasis and is associated with several diseases or cancers in cases of dysregulation and dysbiosis. Research on fecal microbiota profiling and its association with certain cancers has opened new possibilities for preventing and managing tumor progression. One such possibility is fecal microbial transplantation (FMT). Studies show that different composition of urinary microbiota is found in various urinary tract diseases. Gut microbiota can regulate immune response against tumors; therefore, FMT may help modulate gut microbiota in a way that potentially enhances responses to immune checkpoint inhibitors, as suggested by emerging evidence in other cancers, though this needs further validation in PCa. Nevertheless, long-term complications and the safety of FMT are still questioned. We reviewed the roles of gut microbiota in PCa and suggested FMT as a potential tool in the treatment of PCa, which needs further investigations.
{"title":"Advancing prostate cancer treatment: the role of fecal microbiota transplantation as an adjuvant therapy","authors":"Rasoul Ebrahimi , Shahrzad Shahrokhi Nejad , Mehra Fekri , Seyed Aria Nejadghaderi","doi":"10.1016/j.crmicr.2025.100420","DOIUrl":"10.1016/j.crmicr.2025.100420","url":null,"abstract":"<div><div>Prostate cancer (PCa) is a major cause of cancer-related deaths worldwide. While current treatments such as surveillance, surgery, and radiation are effective, they have their limitations. These can include patient incompliance due to side effects or resistance to hormonal changes, highlighting the need for alternative approaches. Human microbiota, a complex and dynamic host, plays a significant role in the homeostasis and is associated with several diseases or cancers in cases of dysregulation and dysbiosis. Research on fecal microbiota profiling and its association with certain cancers has opened new possibilities for preventing and managing tumor progression. One such possibility is fecal microbial transplantation (FMT). Studies show that different composition of urinary microbiota is found in various urinary tract diseases. Gut microbiota can regulate immune response against tumors; therefore, FMT may help modulate gut microbiota in a way that potentially enhances responses to immune checkpoint inhibitors, as suggested by emerging evidence in other cancers, though this needs further validation in PCa. Nevertheless, long-term complications and the safety of FMT are still questioned. We reviewed the roles of gut microbiota in PCa and suggested FMT as a potential tool in the treatment of PCa, which needs further investigations.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100420"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144306647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01Epub Date: 2025-07-09DOI: 10.1016/j.crmicr.2025.100440
Aldo Barrera , Constanza Martínez-Valdebenito , Bruno Nervi , Aracelly Gaete-Argel , Nicolás M.S. Gálvez , Catalina Osses , Cecilia Vizcaya , María E. Ceballos , Jaime Pereira , Mayling Chang , Luis Rojas , Sebastián Mondaca , Carolina Henríquez , Alexis M. Kalergis , Alessandro Sette , Alba Grifoni , Ricardo Soto-Rifo , Fernando Valiente-Echeverría , Marcela Ferres , María E. Balcells , Nicole Le Corre
During the SARS-CoV-2 pandemic, the use of convalescent plasma (CP) in high-risk patients was proposed and widely implemented in several countries as a potential COVID-19 therapy. Nonetheless, CP therapy’s impact on immune response is nowadays poorly understood, including the correlation between IgG levels, neutralization capacity, and cellular immune response against SARS-CoV-2. Here we evaluated, in a cohort of patients with COVID-19 requiring hospitalization and having received or not CP, as well as in CP donors (recovered from mild disease), the humoral and cellular immune response assessed by titers of SARS-CoV-2 IgG, neutralizing antibodies, and IFN-γ+/IL-2+ ELISpot during the first month (early) and up to nine months (long-term) after symptom onset. Results showed higher seropositivity and seroconversion rates between 7–12 days after plasma infusion in CP-recipients. However, similar IgG and neutralizing immune response kinetics between CP-recipients and non-recipients was observed during the first and until the ninth month of analysis. A positive correlation between IgG and neutralizing levels was detected. Compared to outpatient donors, hospitalized individuals showed a higher response at 3 and 6 months after symptoms onset. A sustained SARS-CoV-2-specific CD4+ and CD8+ T cell response was observed in outpatients and hospitalized patients, regardless of the CP treatment. We concluded that the CP infusion did not affect the long-term SARS-CoV-2 specific humoral and cellular immune responses. Nonetheless, CP may provide a therapeutic window by promoting a higher humoral response during the acute phase of COVID-19.
{"title":"Convalescent plasma therapy and long-term SARS-COV-2 antiviral immune response in a prospective cohort of patients with COVID-19","authors":"Aldo Barrera , Constanza Martínez-Valdebenito , Bruno Nervi , Aracelly Gaete-Argel , Nicolás M.S. Gálvez , Catalina Osses , Cecilia Vizcaya , María E. Ceballos , Jaime Pereira , Mayling Chang , Luis Rojas , Sebastián Mondaca , Carolina Henríquez , Alexis M. Kalergis , Alessandro Sette , Alba Grifoni , Ricardo Soto-Rifo , Fernando Valiente-Echeverría , Marcela Ferres , María E. Balcells , Nicole Le Corre","doi":"10.1016/j.crmicr.2025.100440","DOIUrl":"10.1016/j.crmicr.2025.100440","url":null,"abstract":"<div><div>During the SARS-CoV-2 pandemic, the use of convalescent plasma (CP) in high-risk patients was proposed and widely implemented in several countries as a potential COVID-19 therapy. Nonetheless, CP therapy’s impact on immune response is nowadays poorly understood, including the correlation between IgG levels, neutralization capacity, and cellular immune response against SARS-CoV-2. Here we evaluated, in a cohort of patients with COVID-19 requiring hospitalization and having received or not CP, as well as in CP donors (recovered from mild disease), the humoral and cellular immune response assessed by titers of SARS-CoV-2 IgG, neutralizing antibodies, and IFN-γ<sup>+</sup>/IL-2<sup>+</sup> ELISpot during the first month (early) and up to nine months (long-term) after symptom onset. Results showed higher seropositivity and seroconversion rates between 7–12 days after plasma infusion in CP-recipients. However, similar IgG and neutralizing immune response kinetics between CP-recipients and non-recipients was observed during the first and until the ninth month of analysis. A positive correlation between IgG and neutralizing levels was detected. Compared to outpatient donors, hospitalized individuals showed a higher response at 3 and 6 months after symptoms onset. A sustained SARS-CoV-2-specific CD4<sup>+</sup> and CD8<sup>+</sup> T cell response was observed in outpatients and hospitalized patients, regardless of the CP treatment. We concluded that the CP infusion did not affect the long-term SARS-CoV-2 specific humoral and cellular immune responses. Nonetheless, CP may provide a therapeutic window by promoting a higher humoral response during the acute phase of COVID-19.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100440"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144680160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<div><div>This study aimed to evaluate the genomic characteristics of <em>Klebsiella</em> spp. from human, animal, and food sources, and to establish their clonal relationships with globally circulating sequence types (STs). Using both phenotypic and next-generation sequencing approaches, a total of 300 samples comprising food samples (<em>n</em> = 180) and human clinical samples (<em>n</em> = 120) were collected and analyzed. Of these, 45 <em>Klebsiella</em> spp. were isolated from human (<em>n</em> = 16), animal (<em>n</em> = 15), and food (<em>n</em> = 14) sources. <em>K. pneumoniae</em> was the predominant species (34/45; 75.5%), followed by <em>K. variicola</em> subsp<em>. variicola</em> (4/45; 8.8%), <em>K. quasipneumoniae</em> (3/45; 6.6%), <em>K. pneumoniae</em> subsp. <em>similipneumoniae</em> (2/45; 4.4%), <em>K. aerogenes</em> (1/45; 2.2%)<em>,</em> and <em>K. michiganensis</em> (1/45; 2.2%). Considering all the sources, 57.8 % of the isolates resulted in resistant to trimethoprim-sulfamethoxazole, while a lower percentage of strains showed resistance to aztreonam (17.8%), cefpodoxime (17.8%), cefotaxime (22.2%), ceftazidime (22.2%), ciprofloxacin (24.4%), colistin (15.6%), gentamicin (8.9%), levofloxacin (2.2%) and tobramycin (11.1%). In general, resistant strains were detected more frequently in samples of human and animal origin than in those of food origin. A total of 17 distinct STs were identified, including 9 novel STs. The fluoroquinolones resistance was mainly attributed to the presence of gene <em>qnrS1</em> (33%), while <em>strB</em> (22%), <em>strA</em> (17.7%), and <em>aac (6′)-Ibr-cr</em> (11.1%) for aminoglycoside. β-lactam resistance genes <em>bla</em><sub>CTX−</sub><sub>M</sub><em><sub>,</sub> bla</em><sub>SHV</sub>, <em>bla</em><sub>TEM</sub>, <em>bla</em><sub>OXA</sub>, and <em>bla</em><sub>OKP</sub>-<sub>B</sub> were considerably present in human (15/16; 93.7%) and animal (17/19; 89.5%) isolates. Among ESBL-encoding genes, <em>bla</em><sub>OXY-1</sub> (1/10; 10%) was exclusively found in food samples. The emergence of antibiotic-resistant and novel lineages of <em>Klebsiella</em> spp., with identical STs across human, animal, and food niches, indicates clonal expansion of high-risk strains. Surveillance and control of ESBL-producing <em>Enterobacteriaceae</em> using the One Health approach are urgently needed in Northern Nigeria.</div></div><div><h3>Importance</h3><div>. This study contributes to the understanding of the epidemiology of <em>Klebsiella</em> spp. in Nigeria. The study highlights that even in regions with relatively limited use of last resort antibiotics, high-risk global clones are circulating. These findings, aligned with the One Health approach, and emphasize the close interconnection between human, animal, and food sources, which facilitates the spread of common clones. Given the continuous emergence of new resistance mechanisms in <em>Klebsiella</em> spp., ongoing surveillance across Africa is war
{"title":"Antibiotic resistance and novel Sequence Types of Klebsiella spp. in human, animal, and food sources: a One Health perspective from Northern Nigeria","authors":"Ayodele Timilehin Adesoji , Vittoria Mattioni Marchetti , Claudia Cortimiglia , Francesca Piscopiello , Ilaria Petrizzi , Aurora Piazza , Emmanuel Dayo Alabi , Pier Sandro Cocconcelli , Roberta Migliavacca","doi":"10.1016/j.crmicr.2025.100458","DOIUrl":"10.1016/j.crmicr.2025.100458","url":null,"abstract":"<div><div>This study aimed to evaluate the genomic characteristics of <em>Klebsiella</em> spp. from human, animal, and food sources, and to establish their clonal relationships with globally circulating sequence types (STs). Using both phenotypic and next-generation sequencing approaches, a total of 300 samples comprising food samples (<em>n</em> = 180) and human clinical samples (<em>n</em> = 120) were collected and analyzed. Of these, 45 <em>Klebsiella</em> spp. were isolated from human (<em>n</em> = 16), animal (<em>n</em> = 15), and food (<em>n</em> = 14) sources. <em>K. pneumoniae</em> was the predominant species (34/45; 75.5%), followed by <em>K. variicola</em> subsp<em>. variicola</em> (4/45; 8.8%), <em>K. quasipneumoniae</em> (3/45; 6.6%), <em>K. pneumoniae</em> subsp. <em>similipneumoniae</em> (2/45; 4.4%), <em>K. aerogenes</em> (1/45; 2.2%)<em>,</em> and <em>K. michiganensis</em> (1/45; 2.2%). Considering all the sources, 57.8 % of the isolates resulted in resistant to trimethoprim-sulfamethoxazole, while a lower percentage of strains showed resistance to aztreonam (17.8%), cefpodoxime (17.8%), cefotaxime (22.2%), ceftazidime (22.2%), ciprofloxacin (24.4%), colistin (15.6%), gentamicin (8.9%), levofloxacin (2.2%) and tobramycin (11.1%). In general, resistant strains were detected more frequently in samples of human and animal origin than in those of food origin. A total of 17 distinct STs were identified, including 9 novel STs. The fluoroquinolones resistance was mainly attributed to the presence of gene <em>qnrS1</em> (33%), while <em>strB</em> (22%), <em>strA</em> (17.7%), and <em>aac (6′)-Ibr-cr</em> (11.1%) for aminoglycoside. β-lactam resistance genes <em>bla</em><sub>CTX−</sub><sub>M</sub><em><sub>,</sub> bla</em><sub>SHV</sub>, <em>bla</em><sub>TEM</sub>, <em>bla</em><sub>OXA</sub>, and <em>bla</em><sub>OKP</sub>-<sub>B</sub> were considerably present in human (15/16; 93.7%) and animal (17/19; 89.5%) isolates. Among ESBL-encoding genes, <em>bla</em><sub>OXY-1</sub> (1/10; 10%) was exclusively found in food samples. The emergence of antibiotic-resistant and novel lineages of <em>Klebsiella</em> spp., with identical STs across human, animal, and food niches, indicates clonal expansion of high-risk strains. Surveillance and control of ESBL-producing <em>Enterobacteriaceae</em> using the One Health approach are urgently needed in Northern Nigeria.</div></div><div><h3>Importance</h3><div>. This study contributes to the understanding of the epidemiology of <em>Klebsiella</em> spp. in Nigeria. The study highlights that even in regions with relatively limited use of last resort antibiotics, high-risk global clones are circulating. These findings, aligned with the One Health approach, and emphasize the close interconnection between human, animal, and food sources, which facilitates the spread of common clones. Given the continuous emergence of new resistance mechanisms in <em>Klebsiella</em> spp., ongoing surveillance across Africa is war","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100458"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01Epub Date: 2025-09-23DOI: 10.1016/j.crmicr.2025.100474
Hailing Yang , Yanxiu Sha , Chunmei Zhang , Xiuying Li , Yingying Xu , Te Liu
Endometriosis, a complex gynecological disorder characterized by aberrant growth of endometrial tissue outside the uterine cavity, poses a significant challenge to women's health. Emerging evidence implicates environmental pollutants, particularly di-(2-ethylhexyl) phthalate (DEHP), as potential contributors to endometriosis development. However, the precise molecular mechanisms underlying this effect remain poorly understood. Herein, we investigated the role of intestinal Odoribacter/butyric acid-mediated m6A methylation in METTL3/IGF-1 signaling in DEHP-induced epithelial-mesenchymal transition (EMT) and endometriosis in a rat model. Our study demonstrated that DEHP exposure alters the gut microbiota composition, leading to modulation of METTL3-mediated m6A modification in the insulin-like growth factor 1 (IGF-1) pathway. This modification enhances EMT in endometrial cells and promotes endometriotic lesion formation. We used a multi-layered approach, including 16S rRNA sequencing, targeted metabolomics, MeRIP-seq, quantitative polymerase chain reaction, western blotting, and immunohistochemistry, to elucidate the mechanistic role of intestinal Odoribacter/butyric acid pathway-mediated METTL3/IGF-1 m6A modification in DEHP-induced endometriosis. The results revealed a significant shift in microbial diversity and a corresponding increase in METTL3/IGF-1 m6A methylation in DEHP-exposed rats, which was directly linked to EMT markers such as E-cadherin and N-cadherin. Our findings reveal a novel gut microbiota-mediated mechanism by which DEHP exposure drives endometriosis via m6A methylation, providing valuable insights into the environmental and molecular basis of the disease. This study not only advances our understanding of the role of DEHP in endometriosis pathogenesis, but also suggests a putative intestinal Odoribacter–butyrate–METTL3/IGF-1 axis that may contribute to disease progression. However, these associations remain correlative, and causality requires further validation through functional experiments.
{"title":"Di-(2-ethylhexyl) phthalate induces endometriosis by modulating IGF-1 m6A methylation via the intestinal Odoribacter–butyric acid axis in female rats","authors":"Hailing Yang , Yanxiu Sha , Chunmei Zhang , Xiuying Li , Yingying Xu , Te Liu","doi":"10.1016/j.crmicr.2025.100474","DOIUrl":"10.1016/j.crmicr.2025.100474","url":null,"abstract":"<div><div>Endometriosis, a complex gynecological disorder characterized by aberrant growth of endometrial tissue outside the uterine cavity, poses a significant challenge to women's health. Emerging evidence implicates environmental pollutants, particularly di-(2-ethylhexyl) phthalate (DEHP), as potential contributors to endometriosis development. However, the precise molecular mechanisms underlying this effect remain poorly understood. Herein, we investigated the role of intestinal <em>Odoribacter</em>/butyric acid-mediated m6A methylation in METTL3/IGF-1 signaling in DEHP-induced epithelial-mesenchymal transition (EMT) and endometriosis in a rat model. Our study demonstrated that DEHP exposure alters the gut microbiota composition, leading to modulation of METTL3-mediated m6A modification in the insulin-like growth factor 1 (IGF-1) pathway. This modification enhances EMT in endometrial cells and promotes endometriotic lesion formation. We used a multi-layered approach, including 16S rRNA sequencing, targeted metabolomics, MeRIP-seq, quantitative polymerase chain reaction, western blotting, and immunohistochemistry, to elucidate the mechanistic role of intestinal <em>Odoribacter</em>/butyric acid pathway-mediated METTL3/IGF-1 m6A modification in DEHP-induced endometriosis. The results revealed a significant shift in microbial diversity and a corresponding increase in METTL3/IGF-1 m6A methylation in DEHP-exposed rats, which was directly linked to EMT markers such as E-cadherin and N-cadherin. Our findings reveal a novel gut microbiota-mediated mechanism by which DEHP exposure drives endometriosis via m6A methylation, providing valuable insights into the environmental and molecular basis of the disease. This study not only advances our understanding of the role of DEHP in endometriosis pathogenesis, but also suggests a putative intestinal <em>Odoribacter</em>–butyrate–METTL3/IGF-1 axis that may contribute to disease progression. However, these associations remain correlative, and causality requires further validation through functional experiments.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100474"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145218938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Increases in water temperature due to climate change are expected to lead to cyanobacterial blooms in various freshwater bodies, including reservoirs, posing a major challenge in terms of water quality management. Therefore, a detailed understanding of the dynamics of cyanobacteria in water bodies is required to increase our knowledge of cyanobacteria. In this study, we attempted to determine the spatial distribution of cyanobacteria in a water body by acoustic techniques, and to understand the distribution of cyanobacteria and how it is affected by the water environment. At the same time, the validity of acoustic measurements of cyanobacteria was verified. Comparison of the estimated abundance of cyanobacteria by acoustic measurements and the measured pigment values of cyanobacteria showed a positive correlation between them, suggesting that acoustic measurements of cyanobacteria are effective. The field survey provided us with a large number of data and allowed us to map the spatial distribution of cyanobacteria in the water body. The results suggest that cyanobacteria are propagated or transported by the water quality control facilities of the reservoir and the water environment. In particular, unlike natural environments, reservoirs are expected to undergo severe environmental changes due to artificial facilities such as water quality control measures, and it will be important to continue monitoring cyanobacteria on a detailed scale using acoustic techniques. Continued research in this area is anticipated to lead to more effective strategies for managing water bodies and mitigating cyanobacterial blooms.
{"title":"Assessing cyanobacterial spatial distribution in reservoirs using acoustic survey techniques for enhanced water quality management","authors":"Taisei Sugawara , Kenji Minami , Sangyeob Kim , Takashi Inagawa , Jiro Okitsu , Shougo Sakamoto , Tomonori Osugi , Nobuyuki Azuma , Yanhui Zhu , Kazushi Miyashita","doi":"10.1016/j.crmicr.2025.100477","DOIUrl":"10.1016/j.crmicr.2025.100477","url":null,"abstract":"<div><div>Increases in water temperature due to climate change are expected to lead to cyanobacterial blooms in various freshwater bodies, including reservoirs, posing a major challenge in terms of water quality management. Therefore, a detailed understanding of the dynamics of cyanobacteria in water bodies is required to increase our knowledge of cyanobacteria. In this study, we attempted to determine the spatial distribution of cyanobacteria in a water body by acoustic techniques, and to understand the distribution of cyanobacteria and how it is affected by the water environment. At the same time, the validity of acoustic measurements of cyanobacteria was verified. Comparison of the estimated abundance of cyanobacteria by acoustic measurements and the measured pigment values of cyanobacteria showed a positive correlation between them, suggesting that acoustic measurements of cyanobacteria are effective. The field survey provided us with a large number of data and allowed us to map the spatial distribution of cyanobacteria in the water body. The results suggest that cyanobacteria are propagated or transported by the water quality control facilities of the reservoir and the water environment. In particular, unlike natural environments, reservoirs are expected to undergo severe environmental changes due to artificial facilities such as water quality control measures, and it will be important to continue monitoring cyanobacteria on a detailed scale using acoustic techniques. Continued research in this area is anticipated to lead to more effective strategies for managing water bodies and mitigating cyanobacterial blooms.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100477"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145219095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01Epub Date: 2025-06-20DOI: 10.1016/j.crmicr.2025.100426
Zhiyong Wang , Xue Hou , Zhikang Guo , Xue Lei , Mu Peng
Background
Rhodococcus is an important genus of soil bacteria known for its metabolic diversity and environmental adaptability under harsh and contaminated conditions. However, few studies have reported on the selenium metabolism of Rhodococcus species.
Results
Here, we isolated a highly selenite-resistance strain PM1 (up to 100 mM) from a selenium-rich mine in Enshi City. This strain reduced 50 mM sodium selenite by 99 % within 72 h. SEM and XPS revealed that PM1 reduced selenite to selenium nanorods (SeNRs). Phylogenetic analysis identified PM1 as R. qingshengii. The whole genome of strain PM1 was sequenced, and a comparative genome analysis of strain PM1with 64 other genomes of Rhodococcus was performed. Whole genome sequencing identified a total of 97 heavy metal resistance genes in strain PM1. Comparative genomics revealed that Rhodococcus species possess an open pan-genome, indicating adaptability to diverse environments. Genomic analysis revealed a total of 96 putative selenite-reducing proteins in strain PM1. Four gene clusters, involved in the pentose phosphate pathway, iron-sulfur cluster assembly, sulfate reductase cluster, and sulfate transport complex, showed high conservation of sequence identity within these species.
Conclusions
To our knowledge, this research enhances our understanding of high selenite reduction in strain PM1 at genomic level and elucidates the biotechnological applications of selenite-reducing bacteria in environmental remediation.
{"title":"Biodegradation of sodium selenite by a highly tolerant strain Rhodococcus qingshengii PM1: Biochemical characterization and comparative genome analysis","authors":"Zhiyong Wang , Xue Hou , Zhikang Guo , Xue Lei , Mu Peng","doi":"10.1016/j.crmicr.2025.100426","DOIUrl":"10.1016/j.crmicr.2025.100426","url":null,"abstract":"<div><h3>Background</h3><div><em>Rhodococcus</em> is an important genus of soil bacteria known for its metabolic diversity and environmental adaptability under harsh and contaminated conditions. However, few studies have reported on the selenium metabolism of <em>Rhodococcus</em> species.</div></div><div><h3>Results</h3><div>Here, we isolated a highly selenite-resistance strain PM1 (up to 100 mM) from a selenium-rich mine in Enshi City. This strain reduced 50 mM sodium selenite by 99 % within 72 h. SEM and XPS revealed that PM1 reduced selenite to selenium nanorods (SeNRs). Phylogenetic analysis identified PM1 as <em>R. qingshengii</em>. The whole genome of strain PM1 was sequenced, and a comparative genome analysis of strain PM1with 64 other genomes of <em>Rhodococcus</em> was performed. Whole genome sequencing identified a total of 97 heavy metal resistance genes in strain PM1. Comparative genomics revealed that <em>Rhodococcus</em> species possess an open pan-genome, indicating adaptability to diverse environments. Genomic analysis revealed a total of 96 putative selenite-reducing proteins in strain PM1. Four gene clusters, involved in the pentose phosphate pathway, iron-sulfur cluster assembly, sulfate reductase cluster, and sulfate transport complex, showed high conservation of sequence identity within these species.</div></div><div><h3>Conclusions</h3><div>To our knowledge, this research enhances our understanding of high selenite reduction in strain PM1 at genomic level and elucidates the biotechnological applications of selenite-reducing bacteria in environmental remediation.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100426"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144471868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01Epub Date: 2024-12-30DOI: 10.1016/j.crmicr.2024.100337
Iván Pável Moreno-Espíndola, Alonso Gutiérrez-Navarro, Diana Carolina Franco-Vásquez, Daniel Vega-Martínez
This paper reflects on the use of microbial genetic resources in the context of agricultural systems. The benefits of harnessing the diversity of these resources in any agricultural system are highlighted, as well as the importance of knowing and preserving native agrobiodiversity, which is deemed an essential resource for Latin America. In this region, harmful effects of irrational use of agrochemicals and monocultures on the environment, economy, and health have been brought to light. In view of the growing awareness and global interest in the development of bioinputs, rational biodiversity use, environmental crisis, cost of conventional synthetic inputs, and the right to safe and quality food, agriculture requires new tools and effective strategies in its practice. Microbial genetic resources are a potential source of relevant and suitable inputs for this purpose. Using the bibliometric technique of co-occurrence of terms with the VOSviewer tool, an analysis of 60 articles published between 2020 and 2024, collected from databases such as Scopus and Web of Science, was performed. An interest in microbial resources and their potential application in plant nutrition, production of growth regulators, defenses against pests and diseases, and tolerance to limiting environmental conditions can be appreciated. However, elucidating their complex ecological dynamics is necessary to understand them in real production contexts, thus allowing the allocation of relevant technological packages and the fair management of their use and potential benefits.
本文对微生物遗传资源在农业系统中的利用进行了反思。会议强调了在任何农业系统中利用这些资源多样性的好处，以及了解和保护当地农业生物多样性的重要性，这被认为是拉丁美洲的一项重要资源。在本区域，不合理使用农用化学品和单一栽培对环境、经济和健康的有害影响已经暴露出来。鉴于对生物投入品开发、生物多样性合理利用、环境危机、常规合成投入品成本以及安全优质食品权的认识和全球兴趣日益增强，农业在实践中需要新的工具和有效的战略。微生物遗传资源是为此目的提供相关和适当投入的潜在来源。采用文献计量学的术语共现技术和VOSviewer工具，对从Scopus和Web of Science等数据库中收集的2020年至2024年间发表的60篇文章进行了分析。对微生物资源及其在植物营养、生长调节剂的生产、对病虫害的防御和对限制环境条件的耐受性方面的潜在应用感兴趣。然而，阐明其复杂的生态动态是必要的，以便在实际生产环境中了解它们，从而能够分配相关的一揽子技术并公平管理它们的使用和潜在利益。
{"title":"Reflections on microbial genetic resources in agricultural systems","authors":"Iván Pável Moreno-Espíndola, Alonso Gutiérrez-Navarro, Diana Carolina Franco-Vásquez, Daniel Vega-Martínez","doi":"10.1016/j.crmicr.2024.100337","DOIUrl":"10.1016/j.crmicr.2024.100337","url":null,"abstract":"<div><div>This paper reflects on the use of microbial genetic resources in the context of agricultural systems. The benefits of harnessing the diversity of these resources in any agricultural system are highlighted, as well as the importance of knowing and preserving native agrobiodiversity, which is deemed an essential resource for Latin America. In this region, harmful effects of irrational use of agrochemicals and monocultures on the environment, economy, and health have been brought to light. In view of the growing awareness and global interest in the development of bioinputs, rational biodiversity use, environmental crisis, cost of conventional synthetic inputs, and the right to safe and quality food, agriculture requires new tools and effective strategies in its practice. Microbial genetic resources are a potential source of relevant and suitable inputs for this purpose. Using the bibliometric technique of co-occurrence of terms with the VOSviewer tool, an analysis of 60 articles published between 2020 and 2024, collected from databases such as Scopus and Web of Science, was performed. An interest in microbial resources and their potential application in plant nutrition, production of growth regulators, defenses against pests and diseases, and tolerance to limiting environmental conditions can be appreciated. However, elucidating their complex ecological dynamics is necessary to understand them in real production contexts, thus allowing the allocation of relevant technological packages and the fair management of their use and potential benefits.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100337"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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