BMC Microbiology最新文献

{"title":"Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.","authors":"F IJdema, L M Arias-Giraldo, E Vervoort, T Struyf, W Van den Ende, J M Raaijmakers, B Lievens, Jeroen De Smet","doi":"10.1186/s12866-025-04327-3","DOIUrl":"10.1186/s12866-025-04327-3","url":null,"abstract":"<p><strong>Background: </strong>The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.</p><p><strong>Results: </strong>Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.</p><p><strong>Conclusions: </strong>Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"612"},"PeriodicalIF":4.2,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211737","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":"Soil bacteria and fungi diversity analysis reveals effects of sesame (Sesamum indicum L.) under waterlogging stress.","authors":"Pengyu Zhang, Feng Li, Dongyong Wang, Yuan Tian, Yasi Rong, Yin Wu, Feina Zheng, Haixia Qin, Zhengkai Teng, Tongmei Gao, Haiyang Zhang","doi":"10.1186/s12866-025-04371-z","DOIUrl":"10.1186/s12866-025-04371-z","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Sesame is one of the major drought-tolerant oil crops, but its growth and development, soil properties and microbial diversity are susceptible to waterlogging stress, affecting overall sesame yield. However, the Changes in microbial communities and the interactions under waterlogging stress in sesame have not been documented. To address this gap, we investigate the effect of waterlogging stress on soil chemical properties in two sesame varieties at the onset flowering stage. Subsequently, the compositions and diversity of soil microbial communities were analyzed by using bacterial 16 S rRNA and fungal ITS sequencing methods (n = 5).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;In this study, 44,820 bacterial and 2,005 fungal operational taxonomic units were obtained and assigned to 33 bacterial and 16 fungal phyla, respectively. Proteobacteria and Firmicutes tended to be found more under waterlogging stress than normal watering stress. Soil bacterial communities primarily comprised Proteobacteria, Firmicutes, Actinobacteriota and Acidobacteriota, and the soil fungal community was dominated by Ascomycota, Mortierellomycota, Glomeromycota and Basidiomycota. Under waterlogging stress condition, the abundance of Firmicutes and Basidiomycota increased, while Actinobacteriota, Acidobacteriota, Mortierellomycota and Glomeromycota decreased. In the waterlogging-sensitive line SP, the relative abundance of beneficial bacterial genus Pseudomonas was increased under waterlogging stress. Alpha diversity analysis revealed that waterlogging stress had a significantly effect on the ACE, PD-tree and Shannon indexes of bacterial and fungal communities in the soil. While beta diversity analysis indicated that there were significant differences in bacterial and fungal communities in two sesame varieties under waterlogging stress. In addition, waterlogging stress had significant (p &lt; 0.05) effects on soil pH, AP (Available Phosphorus) and AK (Available Potassium) in two sesame varieties. Redundancy analysis results revealed that the correlation between soil pH and AP with soil microbial communities was significantly stronger than that with other factors, and they are the main environmental factors affecting changes in soil structure and microbial communities.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;By systematically investigating the effects of waterlogging stress on the community structure, diversity, and key driving factors of sesame rhizosphere microorganisms, this study not only clarified the response characteristics of dominant rhizosphere microbial groups under waterlogging conditions (such as changes in the relative abundance of specific beneficial bacterial genera) but also revealed the mechanism underlying the association between soil physicochemical properties (e.g., pH, available phosphorus) and microbial community dynamics. This lays a solid core foundation for subsequent in-depth research on the dynamic change patterns of sesame rhizosphe","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"620"},"PeriodicalIF":4.2,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211824","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":"Repression of mab_1999 impairs growth and alters cellular morphology of Mycobacterium abscessus.","authors":"Azizah Fitriana Nurul Ilmi, Pornchai Kaewsapsak, Suwatchareeporn Rotcheewaphan","doi":"10.1186/s12866-025-04319-3","DOIUrl":"10.1186/s12866-025-04319-3","url":null,"abstract":"<p><strong>Background: </strong>Cell division is essential for bacterial survival and represents a promising target for the development of novel antibiotics, particularly in mycobacteria. The role of the division protein FtsL in Mycobacterium abscessus remains poorly understood. This study investigated the effects of MAB_1999, a predicted homolog of FtsL, on the growth and cell division of M. abscessus.</p><p><strong>Method: </strong>To investigate the function of mab_1999, a knockdown mutant was generated via CRISPR interference (CRISPRi). The phenotypic impact of mab_1999 suppression was evaluated, with a focus on its effects on M. abscessus growth, cellular morphology, and antibiotic susceptibility.</p><p><strong>Results: </strong>The putative homolog of FtsL in M. abscessus (MAB_1999) shares 54% amino acid sequence identity with FtsL from M. smegmatis (MSMEG_4234). CRISPRi-mediated repression of mab_1999 expression resulted in cell elongation and growth defects, although complete growth arrest was not observed. Furthermore, reduced mab_1999 expression increased the susceptibility of M. abscessus to β-lactam antibiotics, including ceftriaxone and imipenem.</p><p><strong>Conclusions: </strong>Our findings suggest that mab_1999 is involved in cell division and cell wall integrity in M. abscessus. However, further investigation is necessary to confirm its identity as FtsL and to fully elucidate its role in the cell division process and cell wall synthesis.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"599"},"PeriodicalIF":4.2,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211856","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":"Bacterial community dynamics in spontaneously fermented Ghanaian cereals, legumes, root, tuber and plantain flours.","authors":"Richard Atinpoore Atuna, Fortune Akabanda, Stefan Bletz, Natalie Scherff, Jan Makurat, Ursula Bordewick-Dell, Matthias Lamping, Guido Ritter, Alexander Mellmann, Francis Kweku Amagloh","doi":"10.1186/s12866-025-04342-4","DOIUrl":"10.1186/s12866-025-04342-4","url":null,"abstract":"<p><strong>Background: </strong>Spontaneous fermentation is among the oldest food preservation methods, with evidence of enhancing the nutritional and sensorial qualities of products and the synthesis of health-promoting compounds. However, the bacterial communities responsible for these transformative changes remain poorly understood, notably across diverse indigenous Ghanaian substrates, including grains and starchy roots, tubers, and plantains.</p><p><strong>Method: </strong>The study aimed to examine bacterial community diversity in the spontaneous fermentations of selected Ghanaian raw materials for complementary food, namely maize, millet, sorghum, sweetpotato, cassava, soybean and plantain. Fermentation lasted 48 h, with samples collected at 6-h intervals. The pH and total titratable acidity (TTA) were determined using standard protocols over the fermentation period. DNA was extracted directly from the fermented food samples using ZymoBIOMICS™ kits, and full-length 16 S rDNA sequencing was performed on the Pacific Biosciences Sequel IIe long-read sequencing platform. Data processing involved DADA2 and taxonomic classification against the SILVA database v138.1, with analysis conducted using R version 4.4.3.</p><p><strong>Results: </strong>Fermented cereals exhibited increasing bacterial diversity over time, dominated by Weissella confusa, Enterococcus hirae, and Pediococcus acidilactici. Soybean fermentation showed distinct microbial communities with fluctuating diversity. Starch-rich roots, tubers, and plantain supported the growth of Leuconostoc mesenteroides, Weissella confusa, Gluconobacter frateurii, Fructobacillus fructosus, and Pediococcus pentosaceus. Enterococcus faecium favored acidic conditions, while Weissella confusa and Leuconostoc mesenteroides adapted to the fluctuating pH conditions in specific crop substrates.</p><p><strong>Conclusion: </strong>The fermented flours showed increased bacterial diversity over time, dominated by lactic acid bacteria (LAB) and acetic acid bacteria. The fermentation patterns among the plant-based substrates differed in terms of bacterial behavior and their response to pH and TTA over time. Understanding the bacterial community dynamics not only enhances our knowledge of bacterial ecosystems but also offers a foundation for refining the safety, consistency, and nutritional quality of fermented foods.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"602"},"PeriodicalIF":4.2,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492965/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211673","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":"Antifungal effects of metabolites from Arthrinium sp. 2-65 and identification of main active ingredients.","authors":"Huan Qu, Ershuai Yang, Mei Zuo, Zongze Li, Ludan Dai, Youping Su, Xiu Zhang, Yongbin Cheng, Yihan Chen, Yang Chen","doi":"10.1186/s12866-025-04194-y","DOIUrl":"10.1186/s12866-025-04194-y","url":null,"abstract":"<p><strong>Background: </strong>Using microbes and their metabolites as material to develop new biological fungicides is still vital for pesticide development. Our preliminary study found that the endophytic fungi Arthrinium sp. 2-65 of Thymus mongolicus (Ronniger) Ronniger showed a certain inhibitory effect on pathogenic fungi.</p><p><strong>Results: </strong>In this study, the antifungal activity of Arthrinium sp. 2-65 was evaluated. The ethyl acetate extract of Arthrinium sp. 2-65 exhibited significant inhibitory activity against pathogenic fungi, especially Botrytis cinerea. The main compounds of Arthrinium sp. 2-65 metabolites were isolated and purified, and the two compounds were identified by infrared spectroscopy (IR), high-performance liquid chromatography (HPLC), ¹H nuclear magnetic resonance (NMR), ¹³C NMR, and high-resolution mass spectrometry (HRMS) as 2-hexyl-3-methylmaleic anhydride (A) and 2-carboxymethyl-3-n-hexylmaleic acid anhydride (B).</p><p><strong>Conclusions: </strong>The main compounds (A and B) isolated and characterised from the fermentation broth of Arthrinium sp. 2-65 showed satisfactory inhibitory effects against pathogenic fungi, especially B. cinerea. These compounds could be used as potential molecules for the development of novel pesticides to control grey mould.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"594"},"PeriodicalIF":4.2,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211765","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":"Seasonal and spatial dynamics of the intestinal microbiome in tropical freshwater fish: insights from Astyanax aeneus and Brycon costaricensis in the Peñas Blancas river basin, Costa Rica.","authors":"Manuel Cortez-Martínez, Josmari Medrano-Lozano, Kinndle Blanco-Peña, Francisco Quesada-Alvarado, Frank Solano-Campos","doi":"10.1186/s12866-025-04279-8","DOIUrl":"10.1186/s12866-025-04279-8","url":null,"abstract":"<p><strong>Background: </strong>The intestinal microbiome plays a crucial role in fish development and health, facilitating essential functions such as nutrient uptake, immune system response, and disease resistance. However, the microbial communities of Neotropical freshwater fish, such as Astyanax aeneus and Brycon costaricensis, remain largely unexplored. Understanding how microbiomes vary in relation to environmental gradients is key to identifying potential sentinel species for ecosystem monitoring. To understand the dynamics of bacterial diversity and community structure, we collected intestinal content samples from 165 individuals of both species from six points along the Peñas Blancas river basin, Costa Rica, during the dry and rainy seasons and during an intermediate period.</p><p><strong>Results: </strong>Metabarcoding analysis of the 16 S rRNA gene revealed that the intestinal microbial communities of both species were dominated primarily by the genera Cetobacterium, Clostridium, Romboutsia and Plesiomonas. No significant differences were detected in the relative abundance of taxa, metabolic pathways or community structure between the two species and only at the Dam site, a significant increase in the Shannon index was detected in B. costaricensis. Conversely, distinct differences in microbial network properties were found, with A. aeneus showing a lower clustering coefficient and modularity, a shorter average path length and a greater number of hubs. Site and season influenced the microbial community structure of A. aeneus but not the relative abundance of taxa. Similarly, differentially abundant metabolic pathways, including xenobiotic degradation, were enriched in A. aeneus.</p><p><strong>Conclusions: </strong>The similarities in microbiome diversity and structure in both species could arise from parallels in taxonomy, habitat and diet. However, temporal and spatial shifts in the A. aeneus microbial community structure may be associated with sensitivity to changes in environmental stressors such as precipitation, temperature, and runoff. Microbial network analysis revealed that taxa in A. aeneus are more tightly interconnected and form fewer distinct clusters, making it a promising bioindicator for monitoring water quality and anthropogenic impacts.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"595"},"PeriodicalIF":4.2,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211849","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":"Analysis of human endogenous retrovirus in hepatocellular carcinomas using HERV-Fcount.","authors":"Ya-Sian Chang, Ming-Hon Hsu, Chin-Chun Chung, I-Lu Lai, Ya-Ting Lee, Ju-Chen Yen, Chieh-Min Chang, Ta-Chih Liu, Jan-Gowth Chang","doi":"10.1186/s12866-025-04358-w","DOIUrl":"10.1186/s12866-025-04358-w","url":null,"abstract":"<p><strong>Background: </strong>Human endogenous retroviruses (HERVs) are important in the development of human diseases, including cancers, and comprehensive study for hepatocellular carcinoma (HCC) is lacking.</p><p><strong>Methods: </strong>We analyzed the impacts of HERVs on 254 HCC patients using total RNA sequencing (RNA-seq) and a new approach based on featureCounts (we call it HERV-Fcount), and then evaluated the alterations of HERVs in an HCC cell line after TP53 knockdown and alternative splicing (AS)-related small molecules treatment. We also compared the differences in HERVs detection between the Telescope and HERV-Fcount.</p><p><strong>Results: </strong>In all, 206 HERVs with differential expression are correlated with patient survival and there are 299 genes located near the 206 survival-related differentially expressed (DE) HERVs. There are 14 HERVs whose expression is in the same direction as their nearby genes and also have survival significance. Among these, 11 are positive regulators, with 7 detected by both methods and 4 unique to HERV-Fcount, and 3 are negative regulators, with 2 detected by both methods and 1 unique to HERV-Fcount. Knockdown of TP53 results in dysregulation of survival-related DE HERVs and their nearby genes. The molecule modulating AS can influence the expressions of HERVs by regulating the host genes near HERVs.</p><p><strong>Conclusions: </strong>HERV-Fcount detects HERVs faster than the Telescope. In addition to total RNA-seq, which increases the detection of HERVs and their nearby genes, this phenomenon can also be observed with HERV-Fcount. HERVs activation results in dysregulation of nearby genes that could be associated with HCC development and prognosis.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"613"},"PeriodicalIF":4.2,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211719","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":"Cobalt exposure induces the specific associated-bacterial microbiome potentially contributing to cobalt stress alleviation of the host dinoflagellate Scrippsiella acuminata.","authors":"Lixia Shang, Fengting Li, Zhaobao Wang, Zhangxi Hu, Hanying Zou, Jiaqi Lu, Ying Zhong Tang, Yunyan Deng","doi":"10.1186/s12866-025-04359-9","DOIUrl":"10.1186/s12866-025-04359-9","url":null,"abstract":"<p><p>Dinoflagellates grow in tight association with the bacterial community, which exert impacts on the physiology and ecology of both partners. However, the changes of associated-bacterial microbiome with the physiologies of the host dinoflagellate under specific heavy metals (HMs) stress remain largely unknown. In this study, we characterized the bacterial microbiome associated with the laboratory-cultured dinoflagellate Scrippsiella acuminata, a cosmopolitan bloom-forming species, under different cobalt concentrations, via high-throughput sequencing of 16 S rRNA gene amplicons. The sequencing of a total of 72 Libraries generated 6,047,695 reads which were classified into 31 phyla, 97 classes, 215 orders, 367 families, and 782 genera. We found that cobalt stress could greatly affect the growth of S. acuminata as well as the ASV diversity and community composition of the associated bacterial community. Significant dose-dependent changes in the bacterial community were detected, which were found to be closely correlated with some specific bacterial genera. Excessive cobalt exerted significantly inhibitory effects on microalgae growth-promoting bacteria (Marinobacter, Roseobacter, Mameliella, Leifsonia, Roseovarius, and Stappia). A notable increase in the relative abundance of HM-resistant bacteria with siderophore-producing capacity (Alteromonas, Arthrobacter, Pseudoalteromonas, Brevundimonas, Staphylococcus, Microbacterium, and Bacillus) and/or HM bio-removal potential (Corynebacterium, Pseudomonas, Burkholderia, Rhodococcus, and Gemella) was detected upon elevated cobalt concentrations, which potentially contributed to the cobalt stress alleviation of the dinoflagellate host. Our work provided deeper insights into the relationship between the associated-bacterial assemblage and dinoflagellate, and also broadened the current knowledge pertaining to the potential contributions of bacterial microbiome to the HM tolerance of host alga.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"617"},"PeriodicalIF":4.2,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211675","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":"Diet, nutrient characteristics and gut microbiome between summer and winter drive adaptive strategies of East China sika deer (Cervus nippon kopschi) in the Yangtze River basin.","authors":"Zhiming Cao, Dandan Wang, Yuanzhen Cui, Fuxing Huang, Yuqin Liu, Jie Dai, Wenguo Wu, Zhijian Dai, Jielei Xie, Xuntao Zhu, Xiaolong Hu, Yongtao Xu","doi":"10.1186/s12866-025-04368-8","DOIUrl":"10.1186/s12866-025-04368-8","url":null,"abstract":"<p><strong>Background: </strong>Adaptation of species represents the outcome of interactions between organisms and their environment, as well as a product of natural selection and evolution.</p><p><strong>Method: </strong>To elucidate how East China sika deer in TNNR respond to seasonal climatic selection pressures in the mid-lower Yangtze River basin, we investigated their seasonal adaptive strategies via analyses of dietary nutrition and the gut microbiome, using high-throughput sequencing of the trnL P6-loop of chloroplast and 16S rRNA.</p><p><strong>Results: </strong>In summer, sika deer consumed 174 plant species belonging to 183 genera and 107 families, exhibiting pronounced dietary generalization. Conversely, in winter, they fed on 130 species from 173 genera and 90 families, characterized by dietary specialization. The nutritional composition and availability of plants differed between the two seasons, driven by seasonal changes, which led to corresponding adjustments in foraging strategies. Notably, sika deer maintained a stable balance in nutrient intake across seasons. and industrialization of sika deer breeding in eastern China, whereas α-diversity was higher in winter. Microbiota in both seasons exhibited distinct correlations with consumed plant species and nutrients, but their microbial functions were predominantly enriched in metabolic processes. This pattern indicates that sika deer can flexibly reshape the structural and interaction networks of gut microbiota to enhance adaptive capacity to seasonal shifts. Overall, we demonstrated seasonal dynamics and provided new insights into understanding the diet diversity and nutrition components associated with gut microbiota in the adaptation of sika deer. These results will further facilitate genetic resource conservation, habitat improvement, food plant breeding, wild rescue, and industrialization of sika deer breeding in eastern China.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"626"},"PeriodicalIF":4.2,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211758","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":"Exploring the skin mycobiome in intensive care patients: a pilot study on fungal diversity from axillary and groin swabs.","authors":"Teresa Nascimento, João Inácio, Daniela Guerreiro, Patrícia Patrício, Luís Proença, Cristina Toscano, Helena Barroso","doi":"10.1186/s12866-025-04288-7","DOIUrl":"10.1186/s12866-025-04288-7","url":null,"abstract":"<p><p>The skin mycobiome is a largely unexplored component of the human microbiome, especially in critically ill patients. Fungal colonisation in the Intensive Care Unit (ICU) may be influenced by underlying comorbidities and hospital-related risk factors, potentially impacting patient outcomes. This pilot study aimed to characterize the diversity and abundance of skin fungi in ICU patients during their first week of hospitalization. A total of 35 ICU patients were recruited and divided into two groups: Group 1 (patients with 1-2 comorbidities and ICU risk factors) and Group 2 (patients with more than 2 comorbidities and ICU risk factors). Bilateral axillary-groin swabs were collected on admission day (D1) and after one week of ICU stay (D8) for fungal identification. Culture-based methods and MALDI-TOF MS were initially used, followed by Internal Transcribed Spacer 2 (ITS2) sequencing via the Illumina MiSeq platform for in-depth analysis of fungal communities. Fungal diversity and relative abundance were assessed using standard alpha and beta diversity metrics. Culture and MALDI-TOF MS identified only Candida spp., suggesting limited diversity. ITS2 sequencing revealed that Candida (69.3%) was the most prevalent genus, followed by Penicillium (10.3%) and Cladosporium (4.0%), with Malassezia being rare (0.7%). Diversity analysis indicated a relatively stable fungal community throughout the first week (ANOSIM, p = 0.499), with no significant changes in species richness or community structure. By Day 8, Candida spp. represented 79.9% and 78.9% of the mycobiome in Groups 1 and 2, respectively. Preliminary data suggest that the ICU skin mycobiome is dominated by Candida spp. and exhibits low fungal diversity. These findings provide foundational insight into the skin mycobiome of critically ill patients and underscore the need for further research to elucidate its clinical significance and potential role in patient management.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"589"},"PeriodicalIF":4.2,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190976","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}