Microbiology spectrum最新文献

{"title":"The genetic variation of mitochondrial sequences and pathological differences of <i>Echinococcus multilocularis</i> strains from different continents.","authors":"Baoping Guo, Gang Guo, Wenjing Qi, Malike Aizezi, Chuanchuan Wu, Mengxiao Tian, Adriano Casulli, Wenbao Zhang, Jun Li","doi":"10.1128/spectrum.01318-24","DOIUrl":"10.1128/spectrum.01318-24","url":null,"abstract":"<p><p>Alveolar echinococcosis is a lethal zoonotic disease caused by the fox tapeworm <i>Echinococcus multilocularis</i>. The parasite is widely distributed in the Northern Hemisphere and exhibits low genetic diversity among populations. To compare the differences among four <i>E. multilocularis</i> strains from different geographical locations, namely, Alaska (EM-AK), Japan (EM-JP), Xinjiang (EM-XJ), and Ningxia (EM-NX), their complete mitochondrial (mt) sequences were compared, and their induced pathological lesions were analyzed in mouse models. The complete mt sequence of EM-AK resulted in 0.84%-0.86% variation as compared with the other strains, which had a lower variation. Phylogenetic analysis and parsimony network indicated that EM-AK resulted in 30,000 years of evolutionary distance from the other three strains. EM-AK induced more pathological damage than the other three strains, which was likely to induce more host cell infiltration and acute granuloma in the liver. More importantly, EM-AK produced more protoscoleces than the other three strains, which may impact the transmission dynamics of the parasite. Given the geographical location of four strains, which is far from each other, and also the pathological differences, the strains of <i>E. multilocularis</i> are likely models for addressing the relationship and interfacial immune response between the host and the helminth.IMPORTANCE<i>Echinococcus multilocularis</i> is the causative agent of alveolar echinococcosis, which is considered the most serious parasitic disease in the Northern Hemisphere. There are many genotypes, but the pathogenic and mitochondria sequence and differences are still unclear. Therefore, this study showed both pathological and genetic differences between the four strains of <i>E. multilocularis</i>. EM-AK induced more severe immune responses and especially induced more host cell infiltration, which resulted in more severe granuloma in the liver. EM-JP has metacestode lesions morphologically closer to those of <i>E. granulosus</i> with clear cyst fluid. However, this strain produced much fewer protoscoleces (PSCs). Genetically, EM-AK is more distant from other strains.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0131824"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414699","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}

{"title":"The influence of trace metal supplementation on the presence of ceftriaxone resistance in <i>Enterobacteriaceae</i> in the gastrointestinal tract of dairy cattle.","authors":"Charles-Antoine Martineau, Mélissa Duplessis, Jennifer Ronholm, Renée M Petri","doi":"10.1128/spectrum.01090-24","DOIUrl":"10.1128/spectrum.01090-24","url":null,"abstract":"<p><p>The addition of trace minerals into the diet of lactating cows frequently exceeds national recommendations for industry practices. However, the presence of certain heavy metals, such as zinc and copper, has been shown to exert selection pressure on the gut microbiota, favoring metal resistance and potential co-selection for antimicrobial resistance. To determine whether oversupplementation of dietary zinc alters the gut microbiota of dairy cattle, a cross-over design was used to feed either recommended or surplus levels of dietary zinc (0.89×; high mineral diet) compared to the recommended levels (control diet). Rumen, duodenum, and fecal samples were collected to analyze the 16S rRNA microbial community for diversity and relative abundance, with a greater focus on the <i>Enterobacteriaceae</i> family, while mixed enriched gut content samples were cultured to determine the presence of zinc, copper, and ceftriaxone resistances in gram-negative bacteria. Alpha-diversity analysis showed a decrease in richness and evenness (Simpson index) when cows were in the HIGH treatment (<i>P =</i> 0.0464) and a tendency to decrease (<i>P =</i> 0.0592) diversity according to the Shannon index. Despite alpha-diversity differences, <i>Enterobacteriaceae</i> abundance showed no difference between treatments. For culturing, a tendency (<i>P =</i> 0.0956) for decreased fecal resistance to zinc on MacConkey mixed enriched isolates was observed for the HIGH group. This study showed that there were differences between niches but no significant increase in resistance in response to zinc, copper, and ceftriaxone in the enriched <i>Enterobacteriaceae</i> populations from the rumen, duodenum, and fecal niches and that zinc oversupplementation had minimal impact on gut microbiota communities.</p><p><strong>Importance: </strong>The addition of trace minerals into the diet of lactating cows, at levels exceeding national recommendations, is a common industry practice. However, there are new concerns as the presence of certain heavy metals, such as zinc, has been shown to exert selection pressure on the gut microbiota, favoring metal resistance and potential co-selection for antimicrobial resistance. We evaluated how the addition of zinc in the diet of lactating cows affects the bacterial community's relative abundance and diversity, with a focus on the <i>Enterobacteriaceae</i> family throughout the gastrointestinal tract, due to their importance for human health. Using samples from the rumen, duodenum, and feces, we cultivated gram-negative bacteria from enriched samples in the presence of zinc, copper, and ceftriaxone resistances to confirm phenotype resistances. This study contributes to our understanding of how dairy diets oversupplemented with minerals may alter the microbial community of the animal and could contribute to the dissemination of antibiotic resistance.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0109024"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449495","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}

{"title":"Erratum for Yun et al., \"Risk factors for vancomycin treatment failure in heterogeneous vancomycin-intermediate <i>Staphylococcus aureus</i> bacteremia.","authors":"Ji Hyun Yun, Euijin Chang, Seongman Bae, Jiwon Jung, Min Jae Kim, Yong Pil Chong, Sung-Han Kim, Sang-Ho Choi, Sang-Oh Lee, Yang Soo Kim","doi":"10.1128/spectrum.03314-24","DOIUrl":"10.1128/spectrum.03314-24","url":null,"abstract":"","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0331424"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483212","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}

{"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":"","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":"","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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Involvement of an orphan response regulator of the two-component regulatory system in the formation of physiologically mature sporangia in <i>Actinoplanes missouriensis</i>.","authors":"Takuya Akutsu, Zhuwen Tan, Aiko Hirata, Takeaki Tezuka, Yasuo Ohnishi","doi":"10.1128/spectrum.03272-24","DOIUrl":"10.1128/spectrum.03272-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The actinomycete &lt;i&gt;Actinoplanes missouriensis&lt;/i&gt; forms terminal sporangia that contain dormant sporangiospores. Upon contact with water, sporangia release zoospores through a process called sporangium dehiscence. In this study, we characterized &lt;i&gt;asfR&lt;/i&gt; (&lt;i&gt;AMIS_76070&lt;/i&gt;), which encodes an orphan response regulator receiver domain protein of the two-component regulatory system, as one of 136 genes whose transcription was highly activated during sporangium formation. &lt;u&gt;&lt;i&gt;A&lt;/i&gt;&lt;/u&gt;&lt;i&gt;ctinoplanes&lt;/i&gt; &lt;u&gt;s&lt;/u&gt;porangium &lt;u&gt;f&lt;/u&gt;ormation &lt;u&gt;r&lt;/u&gt;egulator (AsfR) homologs are conserved among &lt;i&gt;Actinoplanes&lt;/i&gt; bacteria. An &lt;i&gt;asfR&lt;/i&gt; null mutant (Δ&lt;i&gt;asfR&lt;/i&gt;) strain formed normally shaped sporangia containing apparently normal dormant spores, but they exhibited defective sporangium dehiscence; the number of spores released from the sporangia of the Δ&lt;i&gt;asfR&lt;/i&gt; strain was four orders of magnitude lower than that from the sporangia of the wild-type strain. This phenotypic change was recovered by introducing &lt;i&gt;asfR&lt;/i&gt; with its own promoter into the Δ&lt;i&gt;asfR&lt;/i&gt; strain. Based on the amino acid sequence and predicted structure, the function of AsfR appeared to be controlled by the phosphorylation of Asp-72. Consistently, the phenotypic change observed in the Δ&lt;i&gt;asfR&lt;/i&gt; strain was not restored by introducing a mutated &lt;i&gt;asfR&lt;/i&gt; (D72N) gene. Three orphan histidine kinases (HKs) in &lt;i&gt;A. missouriensis&lt;/i&gt; were found to interact with AsfR by screening using a bacterial two-hybrid assay. However, gene disruption experiments revealed that these three HKs were not required for sporangium dehiscence in &lt;i&gt;A. missouriensis&lt;/i&gt;. Although the molecular functions of AsfR remain to be elucidated, this study shows that AsfR is involved in the formation of physiologically mature sporangia that are fully prepared to release spores under sporangium dehiscence-inducing conditions.IMPORTANCE&lt;i&gt;Actinoplanes missouriensis&lt;/i&gt; undergoes a life cycle involving complex morphological development, including mycelial growth, sporangium formation and dehiscence, swimming as zoospores, germination, and outgrowth to mycelial growth. In this study, we revealed that a stand-alone response regulator receiver domain protein, AsfR, is required for the formation of physiologically mature sporangia that can release spores under sporangium dehiscence-inducing conditions. &lt;i&gt;A. missouriensis&lt;/i&gt; seems to express genes that are involved in sporangium dehiscence during sporangium formation, considering that an &lt;i&gt;asfR&lt;/i&gt; null mutant produced normally shaped sporangia, but these sporangia were deficient in sporangium dehiscence. Although the molecular functions of AsfR, as well as the histidine kinase(s) that phosphorylates AsfR, remain to be elucidated, identification of AsfR as a possible key regulator for the preparation of the onset and progression of sporangium dehiscence is significant, because almost no proteins involved in the early stages of sporangium dehiscence hav","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0327224"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516147","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}

{"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":"","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":"","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":"","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":"","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":"","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":"","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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}