{"title":"Multi-omics analysis reveals circadian disruption of rumen microbiota and serum metabolites in Tibetan sheep under transport stress.","authors":"Wenhui Tang, Penghui Wang, Ting Jiang, Ningna Chen, Maisui Xue, Yale Chen, Rui Pang, Juanxiang Zhang, Ru Wang, Qiangjun Wang, Jiahong Chen, Chunhuan Ren, Yafeng Huang, Zijun Zhang, Xiao Cheng","doi":"10.1186/s12866-026-05109-1","DOIUrl":"https://doi.org/10.1186/s12866-026-05109-1","url":null,"abstract":"<p><strong>Background: </strong>Off-site fattening of Tibetan sheep is a key strategy to mitigate the effects of high-altitude grassland degradation and winter forage scarcity, promoting sustainable development in plateau animal husbandry. However, transport stress (TS) presents a significant challenge to realizing its benefits. The mechanism by which TS affects the health of Tibetan sheep by regulating rumen microbial and serum metabolite rhythmic changes remains unclear.</p><p><strong>Methods: </strong>This study selected six healthy male Tibetan sheep, aged seven months and of comparable body weight, for the transport experiment. Blood and rumen fluid samples were collected at four-hour intervals during 24-hour periods pre-transport (CON) and post-transport (TS) for serum indicators, serum metabolome, and rumen microbiome analyses.</p><p><strong>Result: </strong>The results showed that TS significantly increased serum concentrations of cortisol (COR), melatonin (MT), lipopolysaccharide-binding protein (LBP), serum amyloid A (SAA), and non-esterified fatty acid (NEFA), while significantly decreasing glucose (GLU), total antioxidant capacity (T-AOC), and glutathione peroxidase (GPx) (P < 0.05). Furthermore, the circadian rhythms of COR, MT, LBP, SAA, NEFA, and GPx were significantly disrupted (ADJ.P < 0.05). TS reduced the proportion of rumen microbial circadian rhythms from 3.46% to 1.99%, with Prevotella, Butyrivibrio, and Ruminococcus losing their circadian rhythmicity in the TS phase (ADJ.P < 0.05). Additionally, TS decreased the proportion of circadian rhythm-regulated serum metabolites from 51.74% to 29.51%. In the TS phase, rhythmically regulated metabolites, including 3',5'-cyclic AMP, fumarate, dopamine, glutathione, and angiotensin (1-7), were enriched in pathways such as oxidative phosphorylation, retinol metabolism, and tryptophan metabolism. Multi-omics analyses demonstrated significant correlations between Ruminococcus and energy metabolites (malic acid, 3',5'-cyclic AMP, fumarate, NEFA), and between Butyrivibrio, Anaeroplasma, and inflammatory/antioxidant markers (glutathione, SAA, LBP). In conclusion, this study reveals that TS induces a homeostatic imbalance in Tibetan sheep by disrupting the circadian rhythms of both the rumen microbiota and host metabolism. These findings provide a theoretical basis and molecular targets for developing interventions to alleviate TS in livestock.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811499","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}
BMC MicrobiologyPub Date : 2026-05-02DOI: 10.1186/s12866-026-05106-4
David Harriman, Alex Ng, Monica Bronowski, Ruixuan Yang, Thien Dang, Karen Sherwood, Christopher Nguan, Aaron Miller, Dirk Lange
{"title":"Urobiome composition after renal transplantation: an exploratory study.","authors":"David Harriman, Alex Ng, Monica Bronowski, Ruixuan Yang, Thien Dang, Karen Sherwood, Christopher Nguan, Aaron Miller, Dirk Lange","doi":"10.1186/s12866-026-05106-4","DOIUrl":"https://doi.org/10.1186/s12866-026-05106-4","url":null,"abstract":"<p><strong>Background: </strong>The urobiome of renal transplant recipients is poorly defined. The purpose of this study was to investigate whether there are characteristic changes in the urobiome between pre- to post-transplant states, at varying degrees of post-transplant allograft function, and between those with acute T-cell mediated rejection (TCMR) versus a non-rejector cohort.</p><p><strong>Patients and methods: </strong>41 patients who consented to have urine stored in our transplant biobank were included in this study: 1) Rejectors (n = 10 pts: 6 borderline, 1 Banff IA, 3 Banff IIA TCMR, mean age: 47.4 ± 12.4 yrs); 2) Women (n = 16 pts; mean age: 49.3 ± 17.3 yrs); 3) Men (n = 15 pts, mean age: 47.5 ± 17.2 yrs). Urine was collected via mid-stream clean-catch technique prior to transplant (n = 21), at the time of TCMR (n = 9; within 1 month of transplant), 1-month (n = 15), and 3-months post-transplant (n = 38). Samples were processed and stored at -80 [Formula: see text] until 16S rRNA sequencing. Alpha diversity, beta diversity, and differential abundance analysis was performed.</p><p><strong>Results: </strong>The urobiome was altered post-transplant, with rejectors gaining Corynebacterium and Pseudomonas at time of rejection, and non-rejectors gaining Lactobacillus among other taxa. Within individuals, post-transplant urobiome composition was ~ 75% dissimilar from pre-transplant (p < 0.001). Urobiome composition differed by sex (p = 0.002), but not by age. Differential abundance analysis based on 3-month post-transplant eGFR revealed consistent loss of Lactobacillus with decreased renal function.</p><p><strong>Conclusions: </strong>Our results suggest that renal transplantation has a strong impact on individual urobiome composition, but not diversity, and microbial imbalance may be associated with acute rejection and post-transplant renal function. Our findings indicate a need for further research into the urobiome during renal transplantation to elucidate its potential as a biomarker of and/or contributor to post-transplant allograft health.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810808","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}
BMC MicrobiologyPub Date : 2026-05-02DOI: 10.1186/s12866-026-05115-3
Xuebing Ren, Xin Song, Hang Zhang, Guangqiang Wang, Fan Xie, Haerlihashi Muhetaerhan, Lianzhong Ai, Yanjun Tian
{"title":"Genomic and transcriptomic analysis reveals chitin metabolic pathways in the marine bacterium Microbulbifer harenosus CGMCC 1.13584<sup>T</sup>.","authors":"Xuebing Ren, Xin Song, Hang Zhang, Guangqiang Wang, Fan Xie, Haerlihashi Muhetaerhan, Lianzhong Ai, Yanjun Tian","doi":"10.1186/s12866-026-05115-3","DOIUrl":"https://doi.org/10.1186/s12866-026-05115-3","url":null,"abstract":"<p><strong>Background: </strong>Chitin is the second most abundant polysaccharide in nature, and its degradation by marine microorganisms plays a critical role in the global carbon and nitrogen cycles. This study investigated the marine bacterium Microbulbifer harenosus CGMCC 1.13584<sup>T</sup> to elucidate its chitin metabolic pathway through genomic and transcriptomic analyses.</p><p><strong>Results: </strong>When cultured with chitin as the carbon source, the strain exhibited an extended lag phase and enhanced extracellular chitinase activity. Genome sequencing revealed the presence of genes involved in both hydrolytic and oxidative chitin degradation pathways. Transcriptomic analysis showed that genes associated with the hydrolytic pathway were significantly upregulated upon chitin induction. In contrast, within the oxidative degradation pathway, only early-stage response genes (such as those encoding LPMOs) were markedly upregulated, while genes involved in subsequent metabolic steps (converting GlcNAc1A to KDG-6-P) did not show significant upregulation. Furthermore, a gene encoding a GH10 domain-containing protein was found to be substantially upregulated during growth on chitin.</p><p><strong>Conclusion: </strong>These findings indicate that Microbulbifer harenosus CGMCC 1.13584<sup>T</sup> utilizes a coordinated chitin degradation mechanism, where the hydrolytic pathway dominates carbon flux during active growth, while the oxidative pathway (via LPMOs) likely provides critical initial structural disruption.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811457","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}
BMC MicrobiologyPub Date : 2026-05-02DOI: 10.1186/s12866-026-05054-z
Zongcheng Cai, Shouquan Fu, Fayi Li, Yunfei Xing, Jun Ma, Enqi Yang, Ran Qin, Quanfang Lei, Jianjun Shi
{"title":"Optimized bio-fertilization drives the synergistic recovery of vegetation productivity and soil multifunctionality by reshaping fungal interaction patterns in degraded alpine mines.","authors":"Zongcheng Cai, Shouquan Fu, Fayi Li, Yunfei Xing, Jun Ma, Enqi Yang, Ran Qin, Quanfang Lei, Jianjun Shi","doi":"10.1186/s12866-026-05054-z","DOIUrl":"https://doi.org/10.1186/s12866-026-05054-z","url":null,"abstract":"<p><strong>Background: </strong>Restoring degraded alpine mining ecosystems is critically constrained by soil infertility and the functional decoupling of plant-soil-microbe interactions. While optimized bio-fertilization represents a promising restoration strategy, the mechanisms linking vegetation recovery, shifts in fungal community structure, and soil multifunctionality (SMF) remain poorly understood.</p><p><strong>Methods: </strong>We conducted a three-year field restoration experiment at the Muli coal mine on the Qinghai-Tibet Plateau to evaluate the integrated responses of plant communities and soil functional networks to various fertilization regimes.</p><p><strong>Results: </strong>The optimized regime (W3J1, comprising 375 kg·hm⁻<sup>2</sup> of forage-specific fertilizer and 350 kg·hm⁻<sup>2</sup> of microbial inoculant) elicited the most robust ecological recovery. By the end of the 2024 growing season, it increased absolute vegetation coverage to 77.31% and enhanced aboveground biomass to a peak of 352.67 g·m⁻<sup>2</sup>. Concurrently, the SMF index in W3J1 reached a peak of 0.95, effectively reversing the functional impairment observed in the degraded control (CK). Furthermore, co-occurrence network analysis revealed enhanced fungal community complexity, with the W3J1 treatment expanding network connectivity to 900 edges (compared to 728 edges in the CK), while the W1J3 treatment achieved the highest OTU richness (693). Notably, excessive nutrient inputs in the W3J3 treatment failed to yield additional benefits, as SMF and fungal diversity indices stabilized or declined due to resource imbalances. Random Forest modeling identified vegetation density as the paramount predictor of fungal diversity. Structural Equation Modeling (SEM, R<sup>2</sup> = 0.67) further elucidated a cascading pathway where fertilization directly promoted fungal diversity (standardized path coefficient β = 0.76) and initiated vegetation establishment, which subsequently facilitated shifts in the fungal community structure and interaction networks.</p><p><strong>Conclusions: </strong>The optimized co-application of microbial agents and fertilizers facilitates ecosystem reconstruction by orchestrating the coupling between vegetation density and fungal stability. This provides a theoretical basis for the sustainable restoration of severely degraded alpine mines.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811505","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":"Correction: Consumption of traditional sardinian fermented milk promotes changes in the rat gut microbiota composition and functions.","authors":"Marcello Abbondio, Antonio Palomba, Monica Serra, Cristina Fraumene, Carola Di Meo, Fabio Marongiu, Rosangela Sau, Daniela Pagnozzi, Ezio Laconi, Alessandro Tanca, Sergio Uzzau","doi":"10.1186/s12866-026-05042-3","DOIUrl":"https://doi.org/10.1186/s12866-026-05042-3","url":null,"abstract":"","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13135269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811211","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}
BMC MicrobiologyPub Date : 2026-05-01DOI: 10.1186/s12866-026-05107-3
Iffat Naz, Mina A Almayouf, Abdul Rehman, Abdul Majid, Abdul Basit, Mubbashir Hussain
{"title":"Molecular detection of Cyclospora cayetanensis in fresh produce and irrigation water in peri-urban settings: a cross-sectional study of the environmental-agricultural interface.","authors":"Iffat Naz, Mina A Almayouf, Abdul Rehman, Abdul Majid, Abdul Basit, Mubbashir Hussain","doi":"10.1186/s12866-026-05107-3","DOIUrl":"https://doi.org/10.1186/s12866-026-05107-3","url":null,"abstract":"<p><strong>Background: </strong>Cyclospora cayetanensis is an important foodborne parasite worldwide, with fresh produce and contaminated irrigation water as major transmission vehicles. In South Asia, environmental surveillance data remain limited. We investigated the occurrence of C. cayetanensis DNA in fresh produce and irrigation water across peri-urban areas of Khyber Pakhtunkhwa, Pakistan, and assessed environmental and farm-level factors associated with contamination.</p><p><strong>Methods: </strong>A cross-sectional study was conducted in Peshawar and Kohat districts from April to September 2025. A total of 420 samples were collected, including 300 fresh produce samples (six commonly consumed vegetables and herbs) and 120 irrigation water samples from canal, tube-well, and mixed sources. Samples were processed using concentration techniques, and detection was performed by nested PCR targeting the 18 S rRNA gene. Structured field questionnaires were used to capture farm-level practices, and logistic regression was applied to identify risk factors.</p><p><strong>Results: </strong>We detected C. cayetanensis DNA in 6.0% of produce (18/300) and 12.5% of irrigation water (15/120; p = 0.028). Canal water (20.0%) was more frequently contaminated than tube-well water (5.0%; OR 4.75; 95% CI: 1.01-22.3). Leafy vegetables and herbs had higher contamination than smooth-surfaced produce (8.0% vs. 2.0%; p = 0.009). In multivariable analysis, canal irrigation (aOR 3.41), proximity to drainage channels ≤ 50 m (aOR 3.98), and use of untreated rinsing water (aOR 2.91) remained independently associated with contamination (all p < 0.05).</p><p><strong>Conclusions: </strong>This study provides among the first molecular evidence of C. cayetanensis contamination at the produce-water interface in peri-urban Khyber Pakhtunkhwa, Pakistan, identifying surface irrigation and poor water management as key risk factors. However, because PCR detects DNA rather than viable organisms, these findings indicate environmental contamination and potential exposure pathways rather than direct infection risk. Sequencing confirmation is needed to exclude cross-amplification of related coccidia.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811477","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}
BMC MicrobiologyPub Date : 2026-05-01DOI: 10.1186/s12866-026-05099-0
Zeynep Yazgan, Gökhan Aygün
{"title":"Evaluation of MALDI-TOF MS for identification of clinical filamentous fungi in a routine mycology laboratory.","authors":"Zeynep Yazgan, Gökhan Aygün","doi":"10.1186/s12866-026-05099-0","DOIUrl":"https://doi.org/10.1186/s12866-026-05099-0","url":null,"abstract":"<p><strong>Background: </strong>MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry) technology has become an effective tool in clinical mycology laboratories in recent years for the identification of pathogenic filamentous fungi.</p><p><strong>Methods: </strong>A total of 527 clinical specimens, comprising samples from both superficial and deep mycoses, were included in this study. Filamentous fungal samples isolated from various clinical specimens and identified using conventional methods between 2017 and 2018 at the Medical Microbiology Mycology Laboratory of Istanbul University-Cerrahpaşa Faculty of Medicine Hospital were analyzed using MALDI Biotyper Bruker Daltonik GmbH Revision 4 and the Filamentous Fungi database v3.0.</p><p><strong>Results: </strong>In the identification of mold samples, the highest scoring identification values were determined with the liquid cultivation and extraction method recommended by MALDI-TOF MS for filamentous fungi. A total of 46 different filament fungi species, including 6 dermatophytes and 40 non-dermatophyte filament fungi species, were identified from the clinical samples in the study. Of the total of 527 clinical samples, 27% (n = 142) were identified as having high reliability in the range of 1.8 to 3, and 20% (n = 103) as having low reliability in the range of 1.6 to 1.79. The total rate of identified filament fungi was successfully determined as 47% (n = 245).</p><p><strong>Conclusions: </strong>In the practical experience of our medical mycology laboratory, we evaluated the current uses of MALDI-TOF MS and their practical application in daily routine. In the identification of mold species obtained from clinical samples by MALDI-TOF, it is important to meticulously prepare sample preparation protocols, use an identification strategy suitable for routine diagnosis, and continuously update libraries using advanced databases.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811442","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}
BMC MicrobiologyPub Date : 2026-05-01DOI: 10.1186/s12866-026-05067-8
Carina Weigel, Daniel Pfeiffer
{"title":"Directional matching of swimming polarity provides a competitive advantage during bacterial magneto-aerotaxis.","authors":"Carina Weigel, Daniel Pfeiffer","doi":"10.1186/s12866-026-05067-8","DOIUrl":"10.1186/s12866-026-05067-8","url":null,"abstract":"<p><strong>Background: </strong>Magnetotactic bacteria (MTB) utilize magnetosomes to align passively with Earth's magnetic field. Magnetic alignment, coupled with flagellar motility and aerotaxis, enables MTB to perform magneto-aerotaxis-a strategy that constrains their movement to a one-dimensional trajectory along geomagnetic field lines, which is believed to optimize their search for low-oxygen niches in aquatic environments. Beyond axially constrained movement, environmental MTB isolates exhibit a hemispherically determined swimming polarity-favoring either magnetic north or south-that has been suggested to facilitate descent into oxygen-depleted zones. However, a systematic and quantitative evaluation of how matching swimming polarity influences navigation toward low-oxygen environments has remained elusive. Here, we employed microcapillary assays to assess the functional significance of polar magneto-aerotaxis in the model organism Magnetospirillum gryphiswaldense.</p><p><strong>Results: </strong>We found that a magnetic field configuration matching the predominant swimming polarity of the population results in an up to fourfold increased peak intensity of the aerotactic band compared to populations with non-matching polarity. Competition assays using fluorescently labeled north- and south-seeking populations confirmed that congruence between swimming polarity and magnetic field orientation markedly improves aerotactic band formation in oxygen gradients. Alongside our main findings, we noted biomagnetism-independent light-induced behavioral responses integrated with aerotaxis, driving collective unidirectional migration along the oxygen gradient.</p><p><strong>Conclusions: </strong>Our results provide quantitative evidence that matching swimming polarity with the magnetic field confers a clear competitive advantage over cells with an incorrect polarity when navigating oxygen gradients. These findings reinforce the role of the geomagnetic field in shaping MTB behavior and highlight the adaptive value of magnetotactic swimming polarity in environmental navigation. Our observation of light‑triggered behavior further suggests the presence of an additional sensing modality complementing magneto‑aerotactic behavior, highlighting the sophisticated sensory capabilities of M. gryphiswaldense.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13154873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811358","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}