Microbiology spectrum最新文献

{"title":"The N-terminus of the <i>Chlamydia trachomatis</i> effector Tarp engages the host Hippo pathway.","authors":"George F Aranjuez, Om Patel, Dev Patel, Travis J Jewett","doi":"10.1128/spectrum.02596-24","DOIUrl":"10.1128/spectrum.02596-24","url":null,"abstract":"<p><p><i>Chlamydia trachomatis</i> (<i>Ct</i>) is an obligate, intracellular Gram-negative bacteria and the leading bacterial sexually transmitted infection in the United States. <i>Chlamydia</i> manipulates the host cell biology using various secreted bacterial effectors during its intracellular development. The early effector <i>t</i>ranslocated <i>a</i>ctin-<i>r</i>ecruiting <i>p</i>hosphoprotein (Tarp), important for <i>Chlamydia</i> entry, has a well-characterized C-terminal region which can polymerize and bundle F-actin. In contrast, not much is known about the function of the N-terminus of Tarp (N-Tarp), though present in many <i>Chlamydia</i> spp. To address this, we use <i>Drosophila melanogaster</i> as an <i>in vivo</i> cell biology platform to study N-Tarp-host interactions. Transgenic expression of N-Tarp in <i>Drosophila</i> results in developmental phenotypes consistent with altered host Salvador-Warts-Hippo signaling, a conserved signaling cascade that regulates host cell proliferation and survival. We studied the N-Tarp function in larval imaginal wing discs, which are sensitive to perturbations in Hippo signaling. N-Tarp causes wing disc overgrowth and a concomitant increase in adult wing size, phenocopying overexpression of the Hippo co-activator Yorkie. N-Tarp also causes upregulation of Hippo target genes. Last, N-Tarp-induced phenotypes can be rescued by reducing the levels of Yorkie or the Hippo target genes <i>CycE</i> and <i>Drosophila inhibitor of apoptosis 1 (Diap1)</i>. Thus, we provide evidence that the N-terminal region of the <i>Chlamydia</i> effector Tarp is sufficient to alter host Hippo signaling and acts upstream of the co-activator Yorkie.</p><p><strong>Importance: </strong>The survival of obligate intracellular bacteria like <i>Chlamydia</i> depends on the survival of the host cell itself. It is not surprising that <i>Chlamydia</i>-infected cells are resistant to cell death, though the exact molecular mechanism is largely unknown. Here, we establish that the N-terminal region of the well-known <i>Ct</i> early effector Tarp can alter Hippo signaling in vivo. Only recently implicated in <i>Chlamydia</i> infection, the Hippo pathway is known to promote cell survival. Our findings illuminate one possible mechanism for <i>Chlamydia</i> to promote host cell survival during infection. We further demonstrate the utility of <i>Drosophila melanogaster</i> as a tool in the study of effector function.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0259624"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586298","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}

{"title":"A novel transcriptional regulator, CdeR, modulates the type III secretion system via c-di-GMP signaling in <i>Dickeya dadantii</i>.","authors":"Alaleh Ghasemi, Xiaochen Yuan, Ching-Hong Yang","doi":"10.1128/spectrum.02655-24","DOIUrl":"10.1128/spectrum.02655-24","url":null,"abstract":"<p><p><i>Dickeya dadantii</i> is a bacterial pathogen that causes soft rot disease in many plant species worldwide, including temperate, subtropical, and tropical regions. This bacterium employs the type III secretion system (T3SS) to manipulate host immune responses. Although cyclic-di-GMP (c-di-GMP), a ubiquitous bacterial second messenger, negatively regulates the expression of T3SS genes in <i>D. dadantii</i>, the underlying mechanism remains unclear. In this study, we identified a potential transcriptional regulator, CdeR, which regulates the T3SS involving c-di-GMP. Through transposon mutagenesis, we discovered that deletion of <i>cdeR</i> in a <i>gcpD</i> mutant background restored T3SS gene expression. GcpD is a diguanylate cyclase responsible for c-di-GMP synthesis, and its deletion led to high T3SS gene expression due to low c-di-GMP. Further analysis revealed that, in the <i>gcpD</i> mutant background, CdeR regulates T3SS by manipulating intracellular c-di-GMP levels, involving another diguanylate cyclase, GcpL, whose expression is upregulated by CdeR. Additionally, we found that removing helical regions within the Helix-Turn-Helix DNA-binding domain of CdeR completely disrupted its regulation of the T3SS, underscoring the essential role of this domain in CdeR's functional activity. This study is the first to identify CdeR as a potential transcriptional regulator involved in T3SS regulation. Our findings provide significant insights into the regulatory mechanisms of T3SS and highlight the complex interactions between bacterial second messengers and transcriptional regulators in pathogenic bacteria.IMPORTANCEBacterial pathogens, such as <i>Dickeya dadantii</i>, must adapt to diverse environmental and host conditions by utilizing intricate regulatory networks to control virulence. This study identifies CdeR, a novel transcriptional regulator, as a crucial factor in modulating the expression of the type III secretion system (T3SS), a key virulence mechanism. Importantly, we show that CdeR operates in a cyclic-di-GMP (c-di-GMP)-dependent manner, linking this second messenger to T3SS regulation in <i>D. dadantii</i> for the first time. Our findings reveal a sophisticated interaction between c-di-GMP signaling and transcriptional regulation, highlighting how these systems collectively drive bacterial virulence. This work advances our understanding of bacterial pathogenesis and opens new avenues for developing targeted strategies to mitigate soft rot disease in crops, potentially improving agricultural productivity and plant health.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0265524"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557397","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}

{"title":"Rapid and sensitive isolation of <i>Campylobacter jejuni</i> using immunomagnetic separation from patient specimens exposed to oxygen.","authors":"So Yeon Kim, Young-Sun Yun, Kwang-Jun Lee, Jonghyun Kim","doi":"10.1128/spectrum.01907-24","DOIUrl":"10.1128/spectrum.01907-24","url":null,"abstract":"<p><p>This study describes a method for detecting <i>Campylobacter jejuni</i> in patient stools with subsequent isolation using antibody-magnetic beads in conjunction with selective culture and PCR. Monoclonal antibodies specific for the flagellin A and major outer membrane protein of <i>C. jejuni</i> were generated; two clones (1C7 and 4B2) were used to coat magnetic beads for immunomagnetic separation (IMS). <i>C. jejuni</i> strain NCTC11168 was recovered from human stool samples spiked with varying concentrations (10¹-10⁵ CFU/mL) by <i>Campylobacter</i> (Campy)-IMS or a conventional culture-based method and plated on modified charcoal-cefoperazone-deoxycholate agar; the number of colonies was enumerated. The detection limits of Campy-IMS and conventional culture-based method with spiked stool samples were 10² and 10⁴ CFU/mL, respectively. The sensitivity of IMS-PCR was 10-10,000-fold higher than that of direct PCR. The recovery rate of <i>C. jejuni</i> from spiked stools stored for 12 to 72 h decreased from 72.3 to 5.9% with Campy-IMS and from 48.5 to 0.1% with the conventional culture-based method. Importantly, of 20 PCR (+)/bacterial culture (-) samples that were diagnosed as probable cases according to general criteria, 95% (19/20) were confirmed positive by Campy-IMS. Thus, this study suggests a solution to overcome the problems caused by the inconsistency between probable and confirmed cases of <i>Campylobacter</i> infection.</p><p><strong>Importance: </strong>The isolation, cultivation, and maintenance of <i>Campylobacter</i> spp. are difficult because of the microaerophilic conditions and specific medium needed. Although selective media are useful for the initial isolation of <i>Campylobacter</i>, subsequent exposure of the sample to oxygen has a detrimental effect on the positive culture rate of <i>Campylobacter</i>, significantly lowering the isolation rate from patient samples. In this study, the detection limit was improved by combining immunomagnetic separation and PCR methods to quickly detect <i>Campylobacter jejuni</i> in clinical patient stool samples using antibody<i>-</i>magnetic beads. Therefore, this study is expected to improve confirmation of <i>C. jejuni</i> infection where diagnosis would previously fail with patient samples because of oxygen exposure, inappropriate diagnostic methods, and interference from other bacteria in the sample.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0190724"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441495","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}

{"title":"Validation of rectal swabbing for total and aerobic gut microbiota study.","authors":"Julie Marin, Paul Albin Bertoye, Andre Birgy, Samira Dziri, Mathilde Lescat","doi":"10.1128/spectrum.01823-24","DOIUrl":"10.1128/spectrum.01823-24","url":null,"abstract":"<p><p>In microbiota research, whole stool sampling is the conventional approach but can be problematic or infeasible for certain patients. This study aims to validate the use of rectal swabbing as an alternative method for microbiota analysis and determine optimal storage conditions suitable for various clinical settings, including intensive care units. We evaluated different sampling techniques and storage temperatures. Our findings indicated that rectal swabs yield microbiota diversity comparable to whole stool samples. Notably, storage conditions significantly impacted microbiota profiles, with increased <i>E. coli</i> and <i>Enterococcus sp</i>. quantifications observed at room temperature (RT). Consequently, we recommend immediate refrigeration of rectal swabs to reliably assess aerobic and total microbiota, particularly for patients requiring urgent care, such as antibiotic treatment.</p><p><strong>Importance: </strong>We developed a pragmatic approach to study total and aerobic gut microbiota, applicable in numerous clinical units, such as intensive care or emergency units, where whole stool sampling is often impractical. This approach employs ESwab devices, which are already commonly used in hospitals.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0182324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449498","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}

{"title":"Persistence and decay of neutralizing antibody responses elicited by SARS-CoV-2 infection and hybrid immunity in a Canadian cohort.","authors":"Amy Nouanesengsy, Anthony Semesi, Kim Quach, Danton Ivanochko, Walter Byrne, Matthew Hwang, Maria-Rosa La Neve, Matilde Leon-Ponte, Alice Litosh, Nicole Wisener, Khosrow Adeli, Aaron Campigotto, Eyal Grunebaum, Allison McGeer, Theo J Moraes, Lusia Sepiashvili, Julia Upton, Jean-Philippe Julien, Upton Allen","doi":"10.1128/spectrum.01333-24","DOIUrl":"10.1128/spectrum.01333-24","url":null,"abstract":"<p><p>A major challenge with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has been assessing the intensity, dynamics, and determinants of the antibody responses after infection and/or vaccination. Therefore, we aimed to characterize the longitudinal dynamics of the antibody responses among naturally infected individuals and individuals who achieved hybrid immunity in a large Canadian cohort. We demonstrate that anti-Spike IgGs and neutralizing antibody dynamics vary greatly among individuals with COVID-19, in peak antibody levels, rate of waning, and longevity of the antibody response. Additionally, we found an association between robust antibody responses and individuals with severe COVID-19 clinical symptoms during the first-month post-symptom onset. For individuals who achieved hybrid immunity, a robust increase in anti-S1 IgGs and neutralizing antibodies followed the first vaccination dose; however, there was a minimal increase in the anti-S1 IgGs and neutralizing antibody titers after administration of the second dose of the vaccine. Furthermore, neutralizing antibodies elicited by the wild-type virus alone were largely ineffective against emerging variants of concern in our natural infection-only cohort, in contrast to a much broader and more robust neutralization profile observed in individuals who achieved hybrid immunity. Our findings emphasize the need for global SARS-CoV-2 vaccination efforts to further sustain protective immune responses required to minimize viral spread and disease severity in the population. As SARS-CoV-2 variants continue to emerge, understanding the interplay between previous infections, vaccine durability, and virus evolution will be critical for guiding ongoing vaccination strategies.</p><p><strong>Importance: </strong>A major challenge with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has been assessing the intensity, dynamics, and determinants of the antibody response after infection and/or vaccination. Our paper addresses this in a large Canadian cohort with antibody responses that were generated by natural infection as well as vaccine in some persons studied.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0133324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449563","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}

{"title":"The establishment and optimization of a <i>Mycoplasma pneumoniae</i> detection system based on ERA-CRISPR/Cas12a.","authors":"Fo Yang, Qianlin Wu, Xiaotong Zeng, Qiuyang Jiang, Shanshan Zhang, Jin Wang, Qi Zhang, Feng Li, Dayong Xu","doi":"10.1128/spectrum.03235-24","DOIUrl":"10.1128/spectrum.03235-24","url":null,"abstract":"<p><p><i>Mycoplasma pneumoniae</i> (MP) is a significant pathogen associated with community-acquired pneumonia, with considerable infectious risks posed, particularly to children and immunocompromised individuals. The current methods for detecting MP in research and clinical settings are recognized as time-consuming, instrument-dependent, and prone to non-specific cross-reactivity. Therefore, the creation of a rapid and sensitive detection method is urgently required. In this study, the MP-ERA-Cas12a system, integrating enzyme restriction amplification (ERA) with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a technology, was introduced. Three detection methods were evaluated: the two-pot system, a modified one-pot system, and a lateral flow assay (LFA) strip-based system. In the one-pot system, the amplification and detection steps were consolidated within a single reaction vessel, effectively minimizing the risk of contamination and false positives that may arise from the handling of multiple tubes. It was observed that the one-pot system generated a fluorescent signal within 1 h and produced 1.6 times higher fluorescence signal intensity compared to the two-pot system, achieving a detection limit of 1 copy/μL. In contrast, the LFA system facilitated rapid on-site screening, with visible band results appearing on the strip within 5 min of the reaction, and a detection limit of 10² copies/μL was achieved. High specificity for MP was demonstrated by all methods. Significant advantages, including rapid processing, the absence of complex instrumentation, and ease of use are offered by this detection system, making it particularly suitable for resource-limited clinical settings. The system is seen as an efficient tool for the early diagnosis of MP, with substantial public health and clinical relevance.</p><p><strong>Importance: </strong>This study successfully combined enzyme restriction amplification (ERA) with the specific detection capabilities of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a. Based on the two-pot system established before, the one-pot system and lateral flow assay (LFA) system were developed for <i>Mycoplasma pneumoniae</i> (MP) detection. The MP-ERA-Cas12a system eliminates the need to open the lid during the reaction, reducing aerosol contamination, and minimizing the risk of false positives. The method does not require the use of advanced instruments or equipment and shows strong specificity while not being affected by other pathogens. As a new method of MP detection, the MP-ERA-Cas12a system has an important practical application prospect.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0323524"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492469","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}

{"title":"Canine distemper virus phylogenetic structure and ecological correlates of infection in mesocarnivores across anthropogenic land use gradients.","authors":"Jonathan Wilson, Samantha Rubio, Liliana C M Salvador, Nicole M Nemeth, Jillian D Fishburn, Nicole L Gottdenker","doi":"10.1128/spectrum.01225-24","DOIUrl":"10.1128/spectrum.01225-24","url":null,"abstract":"<p><p>Anthropogenic land use impacts infectious diseases at the wildlife-domestic-human interface by changing host spatial distribution, behavior, density, and population dynamics. Canine distemper virus (CDV) is a significant cause of morbidity and mortality in many wild and domestic animals. Given the propensity of CDV to infect synanthropic mesocarnivores, it is important to investigate host and environmental factors affecting mesocarnivore CDV infection. Here, we investigated patterns of CDV infection and developed a statistical model to identify environmental variables related to CDV risk in commonly affected mesocarnivores. We sampled carcasses (<i>N</i> = 270) submitted to the Southeastern Cooperative Wildlife Disease Study from January 2019 to December 2022 and sequenced the CDV H-gene of 32 CDV-positive animals. Overall, 158 out of 270 mesocarnivores (58.5%) and four species (raccoon, red fox, gray fox, and striped skunk) were diagnosed with CDV across 13 states. Ripley's K analysis showed positive cases were more spatially clustered at larger distances than expected due to chance. A generalized linear model for CDV-infected animals showed surface imperviousness, precipitation, and subadult/adult age classes were significant positive explanatory variables, but elevation had a significant negative association with CDV infection likelihood. H-gene sequence diversity among wild mesocarnivores in the southeastern United States was geographically separated into groups east and west of the Mississippi River, with only two eastern samples clustering with western groups. By identifying areas of intense human development at the highest risk for CDV, it may be possible to focus surveillance efforts in these areas, allowing for earlier outbreak identification, potentially preventing cross-species CDV transmission.</p><p><strong>Importance: </strong>Anthropogenic land use change can impact infectious disease spread by altering animal distribution and behavior. Canine distemper virus (CDV) is a significant cause of morbidity and mortality in wild and domestic carnivores. This study investigated how land use influences CDV infection in wild carnivores by examining tissues collected between 2019 and 2022 from wild carnivores found dead in the southeastern United States. CDV strains were geographically distinct, with differences between populations east and west of the Mississippi river. Statistical models showed areas with increased human development and higher precipitation had higher CDV risk; however, there was lower risk associated with higher elevations and younger animals. The importance of this study is that it identifies geographic structure of CDV in the southern United States, and identifies land-use associations with potential high-risk areas for CDV transmission-information that is useful for wildlife disease surveillance and control strategies.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0122524"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143542516","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}

{"title":"Gut microbiome and plasma metabolome alterations in ileostomy and after closure of ileostomy.","authors":"Liang Xu, Xiaolong Li, Lang Chen, Haitao Ma, Ying Wang, Wenwen Liu, Anyan Liao, Liang Tan, Xiao Gao, Weidong Xiao, Hua Yang, Guangyan Ji, Yuan Qiu","doi":"10.1128/spectrum.01191-24","DOIUrl":"10.1128/spectrum.01191-24","url":null,"abstract":"<p><p>A temporary loop ileostomy is a routine procedure for protecting the anastomosis in patients undergoing radical resection of rectal cancer. Fecal diversion by a diverting ileostomy may induce microbiota dysbiosis in the defunctioned colon; however, data on temporal and spatial microbiome and metabolome changes in these patients are sparse. Thirty patients who underwent ileostomy closure were enrolled. Fecal and plasma samples were collected successively before ileostomy closure, at the first postoperative defecation, and 1 month postoperatively. The 16S rRNA gene sequencing was used to assess changes in gut microbes, and metabolic components in the plasma were analyzed using global untargeted metabolomics. Advanced data analysis methods were used to examine the differences and correlations between flora and metabolites. The gut microbiota in the ileostomy effluent and defunctioned colon had lesser species diversity and richness, with an abundance of aerobic, gram-negative, and potentially pathogenic bacteria. After the intestinal continuity was restored with routine meal feeding, the gut microbes recovered to a standard composition within 1 month. Moreover, xanthine, traumatic acid, L-glutamine, and norepinephrine levels increased markedly in patients with ileostoma. The ileostomy closure reversed the ileostomy-associated metabolic alterations, including an increased abundance of L-leucine, creatine, and 2-ketobutyric acid. Furthermore, <i>Agathobacter</i> and <i>Peptostreptococcus</i> were most closely associated with the reconstruction of postoperative gut microbes. We described a spatiotemporal map of the intestinal microbial ecological reconstruction and metabolic recovery before and after ileostomy reversal for perioperative intervention in patients with ileostomy closure surgery.</p><p><strong>Importance: </strong>In this paper, the changes in the intestinal microbiome and plasma metabolome before and after temporary ileostomy were reported for the first time, and the dynamic changes in intestinal contents were described. At the same time, the key bacterial genera involved in the reestablishment of microflora after the restoration of intestinal continuity were found, and the key relationship between them and plasma metabolites was also found. More importantly, we found that patients with ileal fistula may be at risk of metabolic imbalance and that this particular metabolic state may potentially affect the course of tumor treatment. Finally, the samples in this study were obtained in their natural state and can be easily applied to the clinic to avoid unnecessary invasive examinations.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0119124"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143542562","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}

{"title":"Differential <i>ex vivo</i> susceptibility of <i>Plasmodium malariae</i> and <i>Plasmodium falciparum</i> clinical isolates from Ghana and Mali to current and lead discovery candidate antimalarial drugs.","authors":"Alamissa Soulama, Fanta Sogore, Felix Ansah, Ousmaila Diakite, Jersley D Chirawurah, Fatoumata O Maiga, Mohamed Maiga, Harry A Danwonno, Brice Campo, Abdoulaye A Djimde, Gordon A Awandare, Lucas N Amenga-Etego, Laurent Dembele, Yaw Aniweh","doi":"10.1128/spectrum.02176-24","DOIUrl":"10.1128/spectrum.02176-24","url":null,"abstract":"<p><p>Non-falciparum species causing malaria in humans are considered neglected in the fight toward malaria elimination. Recent data highlight the increasing contribution of <i>Plasmodium malariae</i> to malaria morbidity and mortality. In this study, the susceptibility of <i>P. malariae</i> and <i>Plasmodium falciparum</i> to current antimalarial drugs was compared to advanced lead candidate drugs using field isolates. The blood samples were collected from the Central region of Ghana and Faladje and Kati in Mali. Following this, an <i>ex vivo</i> drug efficacy assay was conducted by screening mono-infected isolates against a panel of antimalarials. In Ghana, the susceptibility of the two species to most of the current antimalarial drugs was comparable, except for artemether, sulfadoxine, and atovaquone, for which the drugs were less potent against <i>P. malariae</i> than <i>P. falciparum</i> (7.12 vs 2.15 nM, 25.72 vs 7.86 nM, and 10.38 vs 2.51 nM, respectively). In Mali, quinine was significantly more potent against <i>P. malariae</i> than <i>P. falciparum</i> (18.35 and 26.84 nM), and tafenoquine was less potent against <i>P. malariae</i> than <i>P. falciparum</i> (5.50 and 2.85 nM). Among the candidate drugs, except INE963, whose inhibitory potency was comparable between both species, the other compounds significantly inhibited <i>P. malariae</i> more than <i>P. falciparum</i>. The data showed that current drugs investigated against the isolates from Ghana may be suitable for curing <i>P. malariae</i> infections. However, in Mali, chloroquine resistance appeared to have affected the suitability of quinine-based compounds for non-falciparum malaria treatment. Therefore, additional studies are required to establish the efficacy of artemether-lumefantrine for the treatment of <i>P. malariae</i> infections.</p><p><strong>Importance: </strong>One major hurdle to research in the community is our inability to have continuous culture for parasites such as <i>Plasmodium malariae</i> and <i>Plasmodium ovale</i>. These two are common in the West African region and co-occur with <i>Plasmodium falciparum</i> in driving both clinical or asymptomatic infections as either mono-infections or mixed infections. This manuscript is a buildup of our efforts at using <i>ex vivo</i> methods to study the susceptibility of <i>P. malariae</i> and <i>P. falciparum</i> to conventional and lead compounds, comparing the isolates from Ghana and Mali. This is necessary to facilitate drug discovery efforts in combating malaria holistically. The community will greatly see this work as a step in the right direction, stimulating more research into these other parasites causing malaria.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0217624"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586268","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}

{"title":"Diversity in chemical subunits and linkages: a key molecular determinant of microbial richness, microbiota interactions, and substrate utilization.","authors":"Hugh C McCullough, Hyun-Seob Song, Jennifer M Auchtung","doi":"10.1128/spectrum.02618-24","DOIUrl":"10.1128/spectrum.02618-24","url":null,"abstract":"<p><p>Dietary fibers play a significant role in shaping the composition and function of microbial communities in the human colon. Our understanding of the specific chemical traits of dietary fibers that influence microbial diversity, interactions, and function remains limited. Toward filling this knowledge gap, we developed a novel measure, termed Chemical Subunits and Linkages (CheSL) Shannon diversity, to characterize the effects of carbohydrate complexity on human fecal bacteria cultured <i>in vitro</i> under controlled, continuous flow conditions using media that systematically varied in carbohydrate composition. Our analysis revealed that CheSL Shannon diversity demonstrated a strong Pearson correlation with microbial richness across multiple fecal samples and study designs. Additionally, we observed that microbial communities in media with higher CheSL Shannon diversity scores exhibited greater peptide utilization and more connected, reproducible structures in computationally inferred microbial interaction networks. Taken together, these findings demonstrate that CheSL Shannon diversity can be a useful tool to quantify the effects of carbohydrate complexity on microbial diversity, metabolic potential, and interactions. Furthermore, our work highlights how robust and stable community data can be generated by engineering media composition and structure. These studies provide a valuable framework for future research on microbial community interactions and their potential impacts on host health.IMPORTANCEFor the human adult gut microbiota, higher microbial diversity strongly correlates with positive health outcomes. This correlation is likely due to increased community resilience that results from functional redundancy that can occur within diverse communities. While previous studies have shown that dietary fibers influence microbiota composition and function, we lack a complete mechanistic understanding of how differences in the composition of fibers are likely to functionally impact microbiota diversity. To address this need, we developed Chemical Subunits and Linkages Shannon diversity, a novel measure that describes carbohydrate complexity. Using this measure, we were able to correlate changes in carbohydrate complexity with alterations in microbial diversity and interspecies interactions. Overall, these analyses provide new perspectives on dietary optimization strategies to improve human health.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0261824"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567439","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}