Search Results (4,921)

Mustelids are a very diverse carnivoran group, boasting the largest number of carnivoran species today, with the most extreme ecological adaptations. Nevertheless, Neotropical Lyncodontini, one Neotropical mustelid subfamily, is one of the least studied from a genetic and evolutionary perspective. The use of small fragments of three mitochondrial (mt) markers (NADH5, 12S rRNA, and D-loop) proved to be very useful for recovering relevant information on the evolutionary history of Neotropical Lyncodontini species of the genera Galictis and Lyncodon. This study used the largest population sample analyzed to date for G. vittata (13 specimens from Guatemala, Colombia, Ecuador, Peru, Bolivia, and French Guiana) and reports for the first time sequences for three mt markers for L. patagonicus other than the mtCyt-b gene. The main results obtained were the following. (1) The haplotype and nucleotide diversity of G. vittata was lower than these statistics measured in other studies of G. cuja in southern and southeastern Brazil. (2) There was evidence from two analyses of a possible population expansion of the female lineages of G. vittata, which began between 635,000 and 370,000 years ago (ya) (mismatch distribution), whereas another procedure (BSP) detected population growth from 500,000 to 80,000 ya, with a population decrease around 40,000 ya. (3) Three genetically distinct groups were detected within G. vittata. One group was in Central America and northern Colombia, another in French Guiana, and the third in the rest of South America. (4) The origin of Neotropical Lyncodontini was older than in other studies (late Miocene, early Pliocene). (6) Some of the analyses detected a closer relationship between L. patagonicus and G. cuja than the latter with G. vittata. This could show that Galictis might be a paraphyletic genus. (7) Many analyses detected that the L. patagonicus haplotypes were the first to originate in situ in South America before the definitive closure of the isthmus of Panama, followed by those of G. cuja, with G. vittata showing the most recent haplotypes. This could indicate that the origin of the current Neotropical Lyncodontini occurred in the south of South America and that colonization occurred towards the north. Full article

Many uncertainties exist on the epidemiology of the Sarcocystis species infecting wild ruminants. In this study, tongue and/or diaphragm tissues of free-ranging wild Caprinae species (54 Pyrenean chamois, 52 mouflons, 146 Iberian ibexes, and 19 Balearean wild goats) residing in the mountain areas of Spain were selected for Sarcocystis spp. detection and species identification. By light microscopy, Sarcocystis sarcocyst frequency rates were considerably high (85.7% in chamois, 82.7% in mouflon, 52.7% in Iberian ibexes), except for the Balearean wild goat (5.3%), which was investigated for the very first time. One excised sarcocyst of Iberian ibex was subjected to transmission electron microscopy, revealing a sibling S. capracanis ultrastructure. Genomic DNA isolated from 57 sarcocysts excised from the hosts’ tissues was investigated through PCR amplicon sequencing of the 18S rRNA and cox1 genes. As a result, sequences of S. capracanis, S. cornagliai, S. rossii and S. tenella were detected, sharing high identity with conspecific sequences. Phylogenetic analyses confirmed a remarkable clustering of all Sarcocystis species in clades encompassing species transmitted via canids, except S. cornagliai, which is allocated in a clade with species using corvid birds as their definitive hosts. Therefore, a significant degree of interconnection between sylvatic and domestic Sarcocystis epidemiological cycles can be drawn in the study area. Full article

Aquaculture production of Asian seabass is increasingly threatened by recurrent bacterial diseases, while practical vaccination strategies that provide protection against bacterial challenges involving multiple pathogens during extended grow-out periods remain limited. This study evaluated the immunological and protective effects of a sequential mucosal vaccination strategy in juvenile Asian seabass (Lates calcarifer; 200 fish per treatment, distributed among four replicate tanks of 50 fish) against four major bacterial pathogens: Flavobacterium covae, Vibrio harveyi, Vibrio vulnificus, and Photobacterium damselae. The vaccination regimen consisted of two nanoemulsion-based immersion vaccination events administered 14 days apart, followed by three oral chitosan–alginate hydrogel vaccination courses administered for 7, 5, and 3 consecutive days. Bacterial challenge experiments were conducted at three post-vaccination time points using immersion and intraperitoneal injection models. Growth performance and feed conversion were evaluated using replicate-tank means as the experimental units. Sequential vaccination did not significantly affect final body weight, weight gain, average daily gain, specific growth rate, or feed conversion ratio (p > 0.05). Vaccinated fish showed significantly higher antigen-specific IgM levels in skin mucus, intestinal mucus, and serum across the evaluated challenge conditions. Correspondingly, ighm, ighd, and ight expression was increased in the gills, skin, head kidney, and intestine, indicating enhanced immunoglobulin-associated responses in mucosal and lymphoid tissues. Full-length 16S rRNA gene sequencing showed vaccine-associated changes in gill and intestinal bacterial community composition, including a lower relative representation of several challenge-associated taxa and a higher relative representation of selected commensal-associated taxa. Vaccinated fish showed significantly higher cumulative survival following F. covae immersion, mixed V. harveyi/V. vulnificus/P. damselae immersion, and mixed-pathogen injection challenges (p < 0.05). These findings demonstrate that sequential nanoemulsion immersion priming and oral hydrogel boosting enhanced pathogen-specific humoral responses and increased immunoglobulin-gene expression. The sequential vaccination strategy improved survival following a separate Flavobacterium covae challenge and a combined Vibrio harveyi/Vibrio vulnificus/Photobacterium damselae challenge during the experimental period without adversely affecting growth. This needle-free strategy warrants further evaluation under commercial aquaculture conditions. Full article

Non-tuberculous mycobacteria (NTM) are increasingly recognized as opportunistic pathogens, yet accurate species identification remains challenging. In this study, two clinical isolates, 19-857^T and 20-525, obtained from patients with suspected pulmonary tuberculosis in Beijing, were characterized using a polyphasic approach integrating phenotypic, biochemical, chemotaxonomic, and genomic analyses. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains within the genus Mycobacterium, with highest similarity to M. peregrinum DSM 43271^T and M. arcueilense DSM 46715^T. However, whole-genome comparisons via average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) yielded values of 85.8–94.1% and 29.1–54.3%, respectively, against their closest relatives—well below the species delineation thresholds (95–96% for ANI; 70% for dDDH)—while the two isolates shared 98.8% ANI and 90.1% dDDH, confirming their co-assignment to a single novel species. Genomic analysis further revealed a repertoire of genes potentially associated with virulence, including glycopeptidolipid biosynthesis, mce operons, ESX secretion systems, and mycobactin synthesis, alongside antimicrobial resistance determinants against rifampicin, tetracyclines, and β-lactams. Mobile genetic element analysis also uncovered extensive insertion sequences and transposon-related elements with differential distribution between the two strains. Based on the combined evidence, we propose Mycobacterium shunyiense sp. nov., with strain 19-857^T (=CGMCC 38906^T) as the type strain. This discovery expands the understanding of NTM diversity and provides genomic reference data for accurate clinical identification. Full article

Polypropylene microplastics (PP-MPs) are ubiquitous in our daily lives, but their toxicological effects on mammals remain poorly understood. This study investigated the toxicity effects of PP-MPs on C57BL/6 mice using 16S rRNA gene amplicon sequencing and transcriptome sequencing. Female and male mice were randomly classified into the control and PP-MPs-treated groups, respectively, and the experiment lasted for 5 weeks. We found that PP-MPs exposure did not affect the levels of immunoglobulin G (IgG), interleukin-4 (IL-4), and interferon gamma (IFN-γ), indicating that humoral immunity and inflammatory levels were not influenced by PP-MPs treatment. However, PP-MPs exposure reduced the PHA response in female mice, but not in male mice. It also did not alter the wet mass of testicles and ovaries, nor the levels of testosterone and estradiol. Exposure to PP-MPs altered the expression of the testicular genes. G protein-coupled receptor signaling pathways, olfactory receptor activity, and protein digestion and absorption were downregulated in the PP group. Collagen genes (Col9a3, Col11a2, Col27a1, Col26a1, Col7a1) play a significant role in downregulating protein digestion and absorption. In addition, PP-MPs exposure caused a change in beta diversity of gut microbiota, indicating the alteration of their community structure. PP-MPs exposure reduced the relative abundance of the probiotic Lactobacillus. Changes in the gut microbiota may be related to the expression levels of testicular genes. Overall, PP-MPs exposure altered both the community structure of the gut microbiota and the expression levels of testicular genes in mice, and collagen genes may serve as a critical factor influencing testicular function. Full article

This study describes a new species of the newt genus (Tylototriton sheni sp. nov.) from the Huangyan area in Zhongfang County of Hunan Province, China, based on morphological and molecular genetic evidence. Phylogenetic analyses based on mitochondrial 16S rRNA and ND2 gene sequences revealed that the new species forms a monophyletic clade with T. maolanensis and T. broadoridgus, all belonging to the T. asperrimus species group. The new species diagnosed by a combination of following characters: (1) Medium-sized body (SVL 60.9–70.1 mm in males and 74.6–75.5 mm in females); (2) Vomerine teeth in a wide inverted V shape, tips separated; (3) Tubercles on dorsolateral body disconnected, total munbers 16–18; (4) Head length greater than head width; (5) The posterolateral part of the squamosal bears a distinct process extending beyond the posterior margin of the exoccipital; (6) Tips of forelimbs and hindlimbs reaching and slightly overlapping when folded towards the body; (7) Tail shorter than body (TAL/SVL = 0.79–0.91 in males, 0.72–0.75 in females); (8) Fingertips extending beyond the tip of the snout when the forelimbs are stretched forward. This paper summarizes the developmental data of embryos of the new taxon. We propose that the conservation status of the new species should be Critically Endangered (CR) following the IUCN criteria (B1ab iii), and the new species should be included in the List of State Key Protected Wild Animals of China. Immediate protection and supervision of its population are recommended. Full article

Chronic constipation is a prevalent functional gastrointestinal disorder with limited long-term treatment options. This study examined whether a fucoidan preparation derived from Sargassum fusiforme (SF) ameliorates loperamide (LOP)-induced constipation in male ICR mice. SF was administered by oral gavage at 50, 100 or 200 mg/kg/day for 35 days, and constipation was induced with LOP (5 mg/kg) during the final 7 days; the design is therefore preventive rather than therapeutic. Defecation endpoints were recorded at the cage level (n = 3 cages per group) and fecal moisture in individual mice (n = 7 per group), whereas colonic cytokine and myeloperoxidase (MPO) measurements (n = 3–4 per group) and Western blot analyses (n = 3 per group) were performed in a small subset of animals, and histological analyses in n = 6–8 per group. SF increased fecal output and fecal moisture content with increasing dose; at 200 mg/kg the relative fecal number returned to the level of the Vehicle control group, although the absolute daily pellet count remained lower than that of the Vehicle control and of the Positive control group. SF administration was associated with lower colonic TNF-α, IL-6, IL-1β and MPO concentrations, with reduced phosphorylation of p38, JNK and ERK, with higher C-kit and stem cell factor (SCF) levels, with normalization of the LOP-induced increase in aquaporin-3 (AQP3), and with recovery of colonic mucosal thickness and mucin content. 16S rRNA gene sequencing showed a shift in fecal microbiota community structure (PERMANOVA p = 0.0002) and a dose-related increase in the combined relative abundance of Lactobacillus and Bifidobacterium, without a reduction in alpha diversity. These findings indicate that SF ameliorates LOP-induced constipation in male mice and that this effect is accompanied by changes in colonic inflammatory signaling, motility-related protein expression, mucosal architecture and gut microbiota composition. Full article

Background/Objectives: Staphylococcus argenteus is a recently recognized member of the Staphylococcus aureus complex that is almost identical to S. aureus phenotypically and by 16S rRNA gene sequences. Although genomic analyses demonstrate that S. argenteus is phylogenetically distinct from S. aureus, the two species exhibit more than 90% nucleotide identity and routine identification methods—including routine biochemical assays and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)—cannot reliably distinguish between the two. We develop and validate a MALDI-TOF MS-based model for accurate identification of S. argenteus. Methods: A multiplex PCR assay targeting crtM and NRPS genes served as the reference standard. MALDI-TOF MS spectra from 25 S. argenteus and 25 methicillin-susceptible S. aureus (MSSA) isolates were analyzed using ClinProTools to identify characteristic peaks and develop the identification model. The model was validated using 40 S. argenteus and 80 MSSA isolates, then applied to 130 randomly selected clinical isolates. Results: Five characteristic peaks—m/z values 5005, 5285, 5323, 6440, and 6526—were identified. Isolates exhibiting at least 4 of these 5 peaks were classified as S. argenteus; those exhibiting fewer than 4 were classified as S. aureus. The model achieved 100% specificity and 100% sensitivity in both the development and validation phases. In the clinical application phase, the model correctly classified all isolates, whereas conventional MALDI-TOF MS yielded several misidentifications. Conclusions: The identification model, and the simple peak-based rule it is based on, can accurately distinguish S. argenteus from MSSA, offering a practical diagnostic tool for clinical microbiology laboratories. Full article

Background: Antibiotic exposure disrupts gut microbiota and lipid metabolism, hindering healthy poultry farming, especially for medicinal Silky fowls. Given that essential oils are prone to volatilization during the decoction of traditional Chinese medicine, this study evaluated modified Shen Ling Bai Zhu San and its essential oils (SLEO) on growth, lipid metabolism, and intestinal health in Silky fowls. Methods: 540 Silky fowls were divided into CON, ATB, ATB+SLEO, and SLEO groups. The cecal microbiota was analyzed via 16S rRNA sequencing. Results: ATB improved weight gain but increased abdominal fat, liver lipid accumulation, and serum triglycerides/cholesterol. Lipid transporter and metabolism gene expression was upregulated, while CPT1A and PPARα were downregulated. SLEO alone significantly improved intestinal villus morphology, as evidenced by a higher villus height/crypt depth (V/C) ratio compared to the ATB group (p < 0.05), along with reduced mortality and enhanced barrier gene expression, without adverse lipid effects. Antibiotics reduced cecal microbial α/β diversity, which SLEO reversed. Enriched SLEO-associated strains correlated strongly with lipid metabolism. Conclusion: SLEO may serve as an antibiotic alternative, regulating lipid metabolism, reducing fat deposition, maintaining gut microbiota homeostasis, and alleviating antibiotic-induced adverse effects. Full article

Nitrogen is integral to all living systems, but its diverse forms are interconverted dynamically through reductions and oxidations that constitute the nitrogen cycle. Ecosystems gain combined nitrogen by bacterial and archaeal reduction in atmospheric N₂, while combined nitrogen is lost to the atmosphere as nitrogenous gases through denitrification. We sought to characterize the diversity and activity of free-living nitrogen-fixing bacteria or diazotrophs in natural prairie grasslands and the activity of the other steps of the nitrogen cycle through metatranscriptomics. DNA and mRNA were obtained from prairie sites that did not contain any leguminous plants to avoid symbiotic nitrogen fixation. Both 16S rRNA gene and nifH amplicon pools were sequenced to characterize the diversity of diazotrophs, and the expression levels of N-cycle genes were quantified by RNAseq. Nitrogen fixation without and with added carbohydrates was quantified by measuring the incorporation of ¹⁵N₂. The soil samples contained a diversity of diazotrophs, as reflected both by 16S rRNA gene and nifH gene sequences. Carbohydrate amendment of soil samples led to substantial ¹⁵N₂ incorporation, showing that members of the resident microbiota were able to fix nitrogen. However, we did not detect ¹⁵N₂ incorporation in unamended soil samples, pointing to a lack of in situ fixation. The very low levels of nitrogenase gene transcripts supported this finding. In contrast, transcripts for nitrification and denitrification genes were expressed, pointing to a gap in the nitrogen cycle. The prevalence of diazotrophs with undetectable nitrogen fixing activity suggested the absence of available carbohydrates to provide the energy needed. The apparent imbalance in the nitrogen cycle would not be sustainable, so other possible mechanisms of acquiring combined nitrogen should be explored. Full article

Anaplasma platys was recognized as a zoonotic pathogen for canine and human infections. However, there is no confirmed evidence demonstrating the existence of A. platys within hard ticks (Rhipicephalus sanguineus sensu lato) infesting dogs in Southern Taiwan. We conducted a field survey for the detection of Anaplasma infection by screening the R. sanguineus s. l. ticks collected from dogs. Molecular detection was performed via a nested-PCR assay targeting the 16S rRNA gene of Anaplasma. Phylogenetic analyses were performed via neighbor-joining against maximum parsimony methods. The genetic relatedness was analyzed via pairwise distance calculation, using the Kimura 2-parameter model. The A. platys infection was detected in various life stages of R. sanguineus s. l. ticks, with an infection rate of 0.8%, 1.0% and 1.4% in nymphs, males and females, respectively. Monthly prevalence was observed from July to October. The genetic identity of detected Anaplasma strains from Taiwan was phylogenetically affiliated to the A. platys species with a 100% sequence homology verified from different countries. This study reveals the first molecular evidence of a zoonotic pathogen, A. platys, detected in R. sanguineus s. l. ticks from Southern Taiwan. Further investigation focused on the vectorial capacity of R. sanguineus s. l. ticks for transmitting A. platys will be beneficial to reveal the public health importance regarding the potential risk for canine and human infection in Southern Taiwan. Full article

(1) Objective: To characterize structural and functional alterations of gut microbiota in patients with newly diagnosed active pulmonary tuberculosis (ATB), screen differential bacterial taxa associated with Mycobacterium tuberculosis (MTB) infection, and explore tuberculosis-related microbial metabolic alterations via predictive functional profiling. (2) Methods: Fresh morning fecal samples were collected from 33 treatment-naive patients with newly diagnosed ATB (ATB group) and 30 healthy controls (HC group). 16S rRNA gene high-throughput sequencing was performed to compare intergroup differences in gut microbial α/β diversity, taxonomic composition, and predicted KEGG functional profiles. Receiver operating characteristic (ROC) curve analysis was conducted to evaluate the internal discriminative ability of candidate differential genera in this single small cohort. (3) Results: The ATB group showed significantly lower gut microbial α-diversity than healthy controls (all P < 0.05). Principal coordinate analysis (PCoA) based on Bray-Curtis distances combined with permutational multivariate analysis of variance (PERMANOVA) revealed significant overall dissimilarity of gut microbial community structure between the two groups (R² = 0.31, p = 0.005). At the phylum level, the relative abundances of Firmicutes and Bacteroidetes were higher, while Proteobacteria was less abundant in ATB patients relative to HC. At the genus level, Streptococcus, R. gnavus and Parabacteroides were significantly enriched in ATB patients, whereas Bifidobacterium, Pseudomonas, Megamonas and Faecalibacterium were depleted. Linear discriminant analysis effect size (LEfSe) analysis uncovered group-specific signature taxa, with pro-inflammatory genera Streptococcus and R. gnavus markedly enriched in the ATB group. ROC analysis yielded area under the curve (AUC) values of 0.836 for Streptococcus and 0.805 for R. gnavus. Predictive KEGG functional analysis demonstrated obvious intergroup differences in microbial metabolism, with purine and pyrimidine nucleotide metabolism pathways significantly upregulated in the ATB group. (4) Conclusions: Treatment-naive patients with ATB exhibited reduced gut microbial diversity in this small cohort. The enrichment of Streptococcus and R. gnavus, as well as the upregulation of purine and pyrimidine metabolic pathways, are all associated with active MTB infection. Full article

The genus Vibrio contains over 150 species of aquatic origin, some of which are important foodborne pathogens, while others cause diseases in finfish, shellfish and/or coral. Accurate identification of these bacteria is important, but highly challenging given their taxonomic diversity. Here we used a range of methods to identify strains from New Zealand oysters initially identified as Vibrio vulnificus. The API20E kit either misidentified, or failed to identify the strains depending on the database used; comparisons of the 16S rRNA gene sequences could not distinguish them from over 50 exemplars of other Vibrio spp. or Allocatenococcus thiocycli. Elastic light scatter analysis showed clear differences between each of the novel isolates and reference strains of Vibrio parahaemolyticus and V. vulnificus, but limits of the in-house database precluded identification. Our whole-genome sequencing (WGS) pipeline allowed genomes and plasmids to be effectively sequenced to completion, enabling in silico DNA-DNA hybridization analysis with 162 Vibrio spp., which identified the strains as either V. campbellii, or one that may represent a novel species closely related to V. rotiferianus. Genome analysis also revealed a variety of genes found in aquacultural and human pathogens, including V. cholerae. Furthermore, resistance to multiple antibiotic classes was indicated both genetically and phenotypically. The implications for New Zealand aquaculture and public health are discussed. WGS is an effective identification strategy for taxonomically complex bacteria such as Vibrio spp. Full article

Reservoir water and sediments are interconnected but ecologically distinct microbial habitats. Their seasonal bacterial dynamics and assembly processes remain poorly understood in arid and semi-arid regions. We investigated bacterial communities in the water and surface sediments of eight reservoirs in Guyuan, Ningxia, in April, July, and October 2025 using 16S rRNA gene sequencing. Water and sediment communities differed markedly in composition. Sediments had substantially higher α-diversity than water: mean Chao1 and Shannon indices were 3063.12 and 9.98 in sediments, compared with 748.38 and 6.25 in water. Seasonal turnover was stronger in water. Water communities differed significantly between April and July (R² = 0.1139, p = 0.001) and between April and October (R² = 0.0968, p = 0.013), whereas sediment communities did not differ between April and July (R² = 0.0581, p = 0.877). Water communities were also more closely associated with seasonal changes in temperature, pH, and nutrients. βNTI-based null models indicated that water communities were mainly associated with stochastic processes sensu lato, whereas sediments showed a stronger deterministic signal, particularly heterogeneous selection. Sediment co-occurrence networks were more complex; in July, they contained 10,496 edges, compared with 7005 edges in water. Network complexity peaked in July in both habitats. These findings show that sediments act as relatively diverse and stable microbial reservoirs, whereas water communities respond more strongly to seasonal environmental variation. They clarify how habitat and season jointly structure bacterial communities in arid and semi-arid reservoirs. Full article

Eukaryotic algae are an important component of the soil microbial community. However, there is limited knowledge about the seasonal variations in the structure of soil algal communities and the correlations between different algal groups and soil environmental factors. Based on gene sequencing of the 18S rRNA V4 region, the changes in the community structure of eukaryotic algae in three different types of soil (sandy soil, forest soil and grassland soil along urban inland lake (Wuhan, China) coast) across four seasons were analyzed, and the correlations between the major taxonomic groups and environmental factors were examined. The annotated algae were ranked by abundance as follows: Chlorophyta, Bacillariophyta, Charophyta, Cryptista, Rhodophyta, Haptophyta and Glaucophyta. The top seven genera in terms of richness were: Chlamydomonas, Tetracystis, Chlorella, Chlorococcum, Coelastrum, Bracteacoccus and Desmodesmus. All soil samples tended to be neutral to alkaline. Environmental drivers for different groups were also explored. In terms of correlation, the environmental factors most related to Chlorophyta were total nitrogen, total phosphorus, and pH. Total nitrogen and water content were most related to Bacillariophyta and Charophyta. The seasonal differences in soil eukaryotic algal communities are more pronounced than the differences between soil types. Chlorophyta and Bacillariophyta are the two most abundant groups in different seasons and soil types. There is a significant difference in community composition between winter and other seasons. Full article