{"title":"Diagnostic accuracy of the IFN-γ release assay using RD1 immunodominant T-cell antigens for diagnosis of extrapulmonary tuberculosis.","authors":"Setareh Mamishi, Babak Pourakbari, Reihaneh Hosseinpour Sadeghi, Majid Marjani, Shima Mahmoudi","doi":"10.1093/femsle/fnae023","DOIUrl":"10.1093/femsle/fnae023","url":null,"abstract":"<p><p>The diagnosis of extrapulmonary tuberculosis (EPTB) poses a significant challenge, with controversies surrounding the accuracy of IFN-γ release assays (IGRAs). This study aimed to assess the diagnostic accuracy of RD1 immunodominant T-cell antigens, including ESAT-6, CFP-10, PE35, and PPE68 proteins, for immunodiagnosis of EPTB. Twenty-nine patients with EPTB were enrolled, and recombinant PE35, PPE68, ESAT-6, and CFP-10 proteins were evaluated in a 3-day Whole Blood Assay. IFN-γ levels were measured using a Human IFN-γ ELISA kit, and the QuantiFERON-TB Gold Plus (QFT-Plus) test was performed. Predominantly, the patients were of Afghan (62%, n = 18) and Iranian (38%, n = 11) nationalities. Eighteen individuals tested positive for QFT-Plus, accounting for 62% of the cases. The positivity rate for IGRA, using each distinct recombinant protein (ESAT-6, PPE68, PE35, and CFP-10), was 72% (n = 21) for every protein tested. Specifically, among Afghan patients, the positivity rates for QFT-Plus and IGRA using ESAT-6, PPE68, PE35, and CFP-10 were 66.7%, 83.3%, 83.3%, 77.8%, and 88.9%, respectively. In contrast, among Iranian patients, the positivity rates for the same antigens were 54.5%, 54.5%, 54.5%, 63.6%, and 45.5%, respectively. In conclusion, our study highlights the potential of IGRA testing utilizing various proteins as a valuable diagnostic tool for EPTB. Further research is needed to elucidate the underlying factors contributing to these disparities and to optimize diagnostic strategies for EPTB in diverse populations.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140293194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Methane production from the biodegradation of lignite with different sizes by mixed fungi-methanogen microflora.","authors":"Longzhen Gao, Xiao Feng, Yixuan Zhang, Hongguang Guo, Xiaogang Mu, Zaixing Huang, Michael Urynowicz","doi":"10.1093/femsle/fnae037","DOIUrl":"10.1093/femsle/fnae037","url":null,"abstract":"<p><p>Biogenic coalbed methane (CBM) is a developing clean energy source. However, it is unclear how the mechanisms of bio-methane production with different sizes of coal. In this work, pulverized coal (PC) and lump coal (LC) were used for methane production by mixed fungi-methanogen microflora. The lower methane production from LC was observed. The aromatic carbon of coal was degraded slightly by 2.17% in LC, while 11.28% in PC. It is attributed to the proportion of lignin-degrading fungi, especially Penicillium, which was reached 67.57% in PC on the 7th day, higher than that of 11.38% in LC. The results suggested that the limited interaction area in LC led to microorganisms hardly utilize aromatics. It also led the accumulation of aromatic organics in the fermentation broth in PC. Increasing the reaction area of coal and facilitating the conversion of aromatic carbon are suggested means to increase methane production in situ.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141287929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Contributing to an inclusive education for neurodivergent students: sharing reflections, practices, and experiences.","authors":"Giorgia Pigato","doi":"10.1093/femsle/fnae046","DOIUrl":"10.1093/femsle/fnae046","url":null,"abstract":"<p><p>It is estimated that one in seven individuals, more than 15% of the population in the UK, are neurodivergent. In recent years, there has been a notable increase in university students disclosing disabilities, specific learning difficulties, or mental health conditions. Despite this, students with disabilities and learning differences often experience lower levels of well-being compared to their peers, and their completion rates are significantly lower. Two years ago, I was tasked with creating a training program for academic staff to enhance their support for neurodivergent students. In this commentary, I share reflections on what I have learned while developing this training, and I outline effective strategies and approaches that can be implemented in the design and delivery of educational content. I advocate a collaborative approach to training development with neurodivergent students and with colleagues with various roles. The commentary draws upon the Universal Design for Learning framework to advocate for an educational environment that is welcoming and accommodating to all learners. It champions strength-based practices, steering clear of the traditional deficit-focused narratives. My goal with this reflection is to prompt educators to reflect on their teaching methodologies, engage in conversations with their students, and to consider substantial pedagogical changes that prioritize inclusivity over reasonable adjustments.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Li-Juan Zhang, Ning Wang, Wei Huang, Long-Yuan Wu, Bo Song, Su-Ling Wang, Jian-Dong Sheng, Wei Wang
{"title":"Genome-based analysis of biosynthetic potential from antimycotic Streptomyces rochei strain A144.","authors":"Li-Juan Zhang, Ning Wang, Wei Huang, Long-Yuan Wu, Bo Song, Su-Ling Wang, Jian-Dong Sheng, Wei Wang","doi":"10.1093/femsle/fnae097","DOIUrl":"10.1093/femsle/fnae097","url":null,"abstract":"<p><p>Streptomyces rochei is a species of Streptomyces with a diverse range of biological activities. Streptomyces rochei strain A144 was isolated from desert soils and exhibits antagonistic activity against several plant pathogenic fungi. The genome of S. rochei A144 was sequenced and revealed the presence of one linear chromosome and one plasmid. The chromosome length was found to be 8 085 429 bp, with a GC content of 72.62%, while the Plas1 length was 177 399 bp, with a GC content (proportion of guanine and cytosine in DNA sequences) of 69.08%. Comparative genomics was employed to analyse the S. rochei group. There is a high degree of collinearity between the genomes of S. rochei strains. Based on pan-genome analysis, S. rochei has 10 315 gene families, including 4051 core and 2322 unique genes. AntiSMASH was used to identify the gene clusters for secondary metabolites, identifying 33 secondary metabolite genes on the A144 genome. Among them, 18 clusters were found to be >70% identical to known biosynthetic gene clusters (BGCs), indicating that A144 has the potential to synthesize secondary metabolites. The majority of the BGCs were found to be conserved within the S. rochei group, including those encoding polyketide synthases, terpenes, non-ribosomal peptide synthetases, other ribosomally synthesized and post-translationally modified peptides, nicotianamine-iron transporters, lanthipeptides, and a few other types. The S. rochei group can be a potential genetic source of useful secondary metabolites with applications in medicine and biotechnology.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tatjana Kazaka, Nikita Zrelovs, Inara Akopjana, Janis Bogans, Juris Jansons, Andris Dislers, Andris Kazaks
{"title":"Recombinant design of the enzymatically active domain of phage Enc34 endolysin to improve its activity against Gram-negative bacteria.","authors":"Tatjana Kazaka, Nikita Zrelovs, Inara Akopjana, Janis Bogans, Juris Jansons, Andris Dislers, Andris Kazaks","doi":"10.1093/femsle/fnae103","DOIUrl":"10.1093/femsle/fnae103","url":null,"abstract":"<p><p>Endolysins are bacteriophage-encoded peptidoglycan-degrading enzymes with potential applications for treating multidrug-resistant bacterial infections. While exogenously applied endolysins are active against Gram-positive bacteria in their native form, Gram-negative bacteria are protected from such activity of most native endolysins by an outer membrane. However, it was shown that recombinant endolysins can be designed to efficiently lyse Gram-negative bacteria from without as well. During our previous efforts, we purified and structurally characterized the enzymatically active domain (EAD) of phage Enc34 endolysin. In this work, we investigated the lytic potential of products resulting from different variants of fusions involving this EAD with a panel of selected antimicrobial peptides. A set of constructs was generated and expressed in Escherichia coli cells. While most such recombinant proteins accumulated intracellularly, some of them could lyse cells from within and appear in the expression medium. The fusion protein variants produced were purified and tested for their bactericidal activity against Gram-negative bacteria. The best candidate caused rapid degradation of E. coli XL1-Blue cells during the first minutes after addition, reducing the viable cell count more than three-fold. We believe that these results might be helpful in the design of new antibacterial tools.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 MAT1 locus is required for microconidia-mediated sexual fertility in the rice blast fungus.","authors":"Kohtetsu Kita, Momotaka Uchida, Tsutomu Arie, Tohru Teraoka, Hisatoshi Kaku, Yasukazu Kanda, Masaki Mori, Takayuki Arazoe, Takashi Kamakura","doi":"10.1093/femsle/fnae004","DOIUrl":"10.1093/femsle/fnae004","url":null,"abstract":"<p><p>Rice blast fungus (Pyricularia oryzae) is a heterothallic ascomycete that causes the most destructive disease in cultivated rice worldwide. This fungus reproduces sexually and asexually, and its mating type is determined by the MAT1 locus, MAT1-1 or MAT1-2. Interestingly, most rice-infecting field isolates show a loss of female fertility, but the MAT1 locus is highly conserved in female-sterile isolates. In this study, we performed a functional analysis of MAT1 using the CRISPR/Cas9 system in female- and male-fertile isolates and female-sterile (male-fertile) isolates. Consistent with a previous report, MAT1 was essential for sexual reproduction but not for asexual reproduction. Meanwhile, deletion mutants of MAT1-1-1, MAT1-1-2, and MAT1-1-3 exhibited phenotypes different from those of other previously described isolates, suggesting that the function of MAT1-1 genes and/or their target genes in sexual reproduction differs among strains or isolates. The MAT1 genes, excluding MAT1-2-6, retained their functions even in female-sterile isolates, and deletion mutants lead to loss or reduction of male fertility. Although MAT1 deletion did not affect microconidia (spermatia) production, microconidia derived from the mutants could not induce perithecia formation. These results indicated that MAT1 is required for microconidia-mediated male fertility in addition to female fertility in P. oryzae .</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139671612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Methylocystis dominates methane oxidation in glacier foreland soil at elevated temperature.","authors":"Xinshu Zhu, Yongcui Deng, Yongqin Liu","doi":"10.1093/femsle/fnae011","DOIUrl":"10.1093/femsle/fnae011","url":null,"abstract":"<p><p>Methane-oxidizing bacteria (methanotrophs) play an important role in mitigating methane emissions in various ecological environments, including cold regions. However, the response of methanotrophs in these cold environments to extreme temperatures above the in-situ temperature has not been thoroughly explored. Therefore, this study collected soil samples from Longxiazailongba (LXZ) and Qiangyong (QY) glacier forelands and incubated them with 13CH4 at 35°C under different soil water conditions. The active methanotroph populations were identified using DNA stable isotope probing (DNA-SIP) and high throughput sequencing techniques. The results showed that the methane oxidation potential in LXZ and QY glacier foreland soils was significantly enhanced at an unusually high temperature of 35°C during microcosm incubations, where abundant substrate (methane and oxygen) was provided. Moreover, the influence of soil water conditions on this potential was observed. Interestingly, Methylocystis, a type II and mesophilic methanotroph, was detected in the unincubated in-situ soil samples and became the active and dominant methanotroph in methane oxidation at 35°C. This suggests that Methylocystis can survive at low temperatures for a prolonged period and thrive under suitable growth conditions. Furthermore, the presence of mesophilic methanotrophs in cold habitats could have potential implications for reducing greenhouse gas emissions in warming glacial environments.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139898003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chenrui Hou, Xuexue Wang, Jianguang Guo, Chunling Qi, Ying Zhang, Yun Chen, Jiao Feng, Bin Zhao, Fei Li
{"title":"Isolation, characterization, and genomic analysis of BUCT627: a lytic bacteriophage targeting Stenotrophomonas maltophilia.","authors":"Chenrui Hou, Xuexue Wang, Jianguang Guo, Chunling Qi, Ying Zhang, Yun Chen, Jiao Feng, Bin Zhao, Fei Li","doi":"10.1093/femsle/fnae076","DOIUrl":"10.1093/femsle/fnae076","url":null,"abstract":"<p><p>Stenotrophomonas infections pose significant therapeutic challenges due to escalating resistance to antibiotics and chemotherapeutic agents. Phages offer a potential solution by virtue of their specific bacterial targeting capabilities. In this study, we isolated a new Stenotrophomonas bacteriophage, named BUCT627, from hospital sewage. Phage BUCT627 exhibited a 30-min latent period and demonstrated a burst size of 46 plaque forming unit (PFU)/cell. Remarkably, this phage displayed robust stability across a wide pH range (pH 3-13) and exhibited resilience under varying thermal conditions. The receptor of phage BUCT627 on Stenotrophomonas maltophilia No. 826 predominantly consist of surface proteins. The complete genome of phage BUCT627 is a 61 860-bp linear double-stranded DNA molecule with a GC content of 56.3%, and contained 99 open reading frames and two tRNAs. Notably, no antibiotic resistance, toxin, virulence-related genes, or lysogen-formation gene clusters was identified in BUCT627. Transmission electron microscopy and phylogeny analysis indicated that this phage was a new member within the Siphoviridae family. The results of this study will enhance our understanding of phage diversity and hold promise for the development of alternative therapeutic strategies against S. maltophilia infections.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zelin Wang, Kaifang Liu, Yuan Du, Danhong Chen, Ting Li, Yuan Chi, Song Zhang, Rongxiao Che, Dong Liu
{"title":"Biological soil crusts significantly improve soil fertility and change soil microbiomes in Qinghai-Tibetan alpine grasslands.","authors":"Zelin Wang, Kaifang Liu, Yuan Du, Danhong Chen, Ting Li, Yuan Chi, Song Zhang, Rongxiao Che, Dong Liu","doi":"10.1093/femsle/fnae088","DOIUrl":"10.1093/femsle/fnae088","url":null,"abstract":"<p><p>Biological soil crusts (BSCs), a vital component of ecosystems, are pivotal in carbon sequestration, nutrient enrichment, and microbial diversity conservation. However, their impact on soil microbiomes in alpine regions remains largely unexplored. Therefore, this study aimed to determine the influence of BSCs on alpine grassland soil microbiomes, by collecting 24 pairs of soils covered by biological and physical crusts along a transect on the Qinghai-Tibetan Plateau. We found that BSCs significantly increased the contents of soil moisture, organic carbon, total nitrogen, and many available nutrients. They also substantially altered the soil microbiomes. Specifically, BSCs significantly increased the relative abundance of Cyanobacteria, Verrucomicrobiota, and Ascomycota, while decreasing the proportions of Gemmatimonadota, Firmicutes, Nitrospirae, Mortierellomycota, and Glomeromycota. By contrast, microbial abundance and α-diversity demonstrated low sensitivity to BSCs across most study sites. Under the BSCs, the assembly of prokaryotic communities was more affected by homogeneous selection and drift, but less affected by dispersal limitation. Conversely, soil fungal community assembly mechanisms showed an inverse trend. Overall, this study provides a comprehensive understanding of the effects of BSCs on soil properties and microbial communities, offering vital insights into the ecological roles of BSCs.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Species diversity and network diversity in the human lung cancer tissue microbiomes.","authors":"Yuting Qiao, Jiandong Mei, Zhanshan Sam Ma","doi":"10.1093/femsle/fnae087","DOIUrl":"10.1093/femsle/fnae087","url":null,"abstract":"<p><p>This study explores the relationship between microbial diversity and disease status in human lung cancer tissue microbiomes, using a sample size of 1212. Analysis divided the data into primary tumour (PT) and normal tissue (NT) categories. Differences in microbial diversity between PT and NT were significant in 57% of comparisons, although dataset dependence was a factor in the diversity levels. Shared species analysis (SSA) indicated no significant differences between PT and NT in over 90% of comparisons. Network diversity assessments revealed significant differences between NT and PT regarding species relative abundances and network link abundances for q = 0-3. Additionally, significant variations were found between NT and lung squamous cell carcinoma (LUSC) at q = 0. in network link probabilities, illustrating the diversity in species interactions. Our findings suggest a stable overall microbiome diversity and composition in lung cancer patients' lung tissues despite patients with diagnosed lung tumours, indicating modified microbial interactions within the tumour. These results highlight an association between altered microbiome interaction patterns and lung tumours, offering new insights into the ecological dynamics of lung cancer microbiomes.</p>","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}