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Keywords = 16S rRNA amplicon sequencing

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17 pages, 7264 KB  
Article
Alterations in Vaginal Microbiota Associated with Pregnancy Outcomes in Dairy Cows Revealed by 16S rRNA Gene Sequencing
by Tong Yu, Xiaoge Zhang, Qiuyu Meng, Feng Yang, Yaqi Zhang, Yujie Tang, Xiaoting Zhu, Yangguang Li, Shikun Wang and Zijing Zhang
Microorganisms 2026, 14(8), 1718; https://doi.org/10.3390/microorganisms14081718 - 5 Aug 2026
Abstract
Early embryonic loss remains a major limitation to reproductive efficiency in dairy cows, with approximately 30–40% of embryonic mortality occurring within 21 days after artificial insemination (AI), ultimately reducing conception rates and economic profitability in dairy production. Increasing evidence suggests that reproductive tract [...] Read more.
Early embryonic loss remains a major limitation to reproductive efficiency in dairy cows, with approximately 30–40% of embryonic mortality occurring within 21 days after artificial insemination (AI), ultimately reducing conception rates and economic profitability in dairy production. Increasing evidence suggests that reproductive tract microorganisms may contribute to pregnancy establishment; however, their functions during early gestation in dairy cows remains poorly understood. In this study, 16S rRNA gene amplicon sequencing was used to characterize vaginal microbiota profiles in multiparous Holstein dairy cows at 7.5 and 21 days after AI, with comparisons performed between pregnant and non-pregnant cows. Significant differences in microbial community structure were observed between pregnancy states. At 7.5 days post-AI, distinct differences in microbial composition were detected at the phylum level, with Bacillota, Bacteroidota, and Pseudomonadota identified as dominant phyla. The relative abundance of Bacillota was higher in pregnant cows, whereas Pseudomonadota was enriched in non-pregnant cows. At the genus level, Ureaplasma was significantly increased in pregnant cows, while Streptococcus and Actinobacillus were significantly enriched in non-pregnant cows. By 21 days after AI, beta diversity analysis revealed a highly significant separation in microbial community structure between pregnant and non-pregnant cows (p < 0.01). Volcano plot and LEfSe analyses further identified representative microbial taxa associated with pregnancy status. Notably, inflammatory-associated genera, including Streptococcus and Actinobacillus, were predominantly enriched in non-pregnant cows, whereas pregnancy-associated taxa, including Ureaplasma and Bifidobacterium, were enriched in pregnant cows. Collectively, early alterations in the vaginal microbiota after AI were closely associated with pregnancy outcomes. These findings provide insight into the microbial associations related to early pregnancy outcomes and may facilitate the identification of potential microbial biomarkers for predicting pregnancy success in dairy cows. Full article
(This article belongs to the Special Issue Advances in Veterinary Microbiology—2nd Edition)
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16 pages, 1893 KB  
Article
Rapid Post-Recovery Changes in the Gill Holobiont of the Deep-Sea Mussel Gigantidas haimaensis During Short-Term Ex Situ Maintenance
by Gaoyou Yao, Yuyuan Wu, Mengfan Ren, Xusheng Guo, Hua Zhang, Haijun Tian, Hanzhi Xu and Maoxian He
Biology 2026, 15(15), 1305; https://doi.org/10.3390/biology15151305 - 5 Aug 2026
Abstract
While chemosymbiosis offers deep-sea bathymodioline mussels a critical metabolic advantage, this dependence makes them vulnerable when removed from their native environment, and their early post-recovery dynamics remain poorly resolved. We maintained adult Gigantidas haimaensis collected from the Haima cold seep at atmospheric pressure [...] Read more.
While chemosymbiosis offers deep-sea bathymodioline mussels a critical metabolic advantage, this dependence makes them vulnerable when removed from their native environment, and their early post-recovery dynamics remain poorly resolved. We maintained adult Gigantidas haimaensis collected from the Haima cold seep at atmospheric pressure and sampled gill tissues at 0, 3 and 9 h after collection. Coupled 16S rRNA amplicon sequencing and RNA-Seq were used to follow changes in the gill microbiota, host transcription and descriptive temporal covariation. Methyloprofundus remained the dominant bacterial genus throughout the experiment, whereas Ca. Vesicomyosocius, the SUP05 cluster, and operational taxonomic units (OTUs) assigned to Vibrio and Pseudoalteromonas had higher relative abundances at 9 h in the descriptive analysis and exhibited positive temporal covariation. RNA-Seq showed a stronger transcriptional shift at 3 h than at 9 h. Stress-related genes, including HSP70, HSP105, Toll-like receptors, fibrinogen-related proteins, dual oxidase, thioredoxin-system genes, ferritin, taurine transporter and sulfide:quinone oxidoreductase, changed markedly, while energy-consuming ribosome biogenesis was suppressed to conserve energy under combined physical and nutritional stressors. The temporal patterns of Ca. Vesicomyosocius and other low-abundance bacterial signals coincided with broad host stress and immune and metabolic transcriptional changes; gene-level microbiome–transcriptome associations were exploratory and did not survive false-discovery-rate (FDR) correction. These results document rapid short-term transcriptional and microbiome changes after recovery, while their causal drivers and consequences require controlled validation. Full article
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17 pages, 1168 KB  
Article
Eisenia andrei and Tenebrio molitor Divergently Restructure the Bacteriome and Mycobiome of Sewage Sludge with Contrasting Biosafety Consequences
by Eduardo Mancilla, Marcos Pérez-Losada, Manuel Aira and Jorge Domínguez
BioTech 2026, 15(3), 62; https://doi.org/10.3390/biotech15030062 - 3 Aug 2026
Viewed by 104
Abstract
The use of invertebrates for sewage sludge bioconversion offers a sustainable strategy for waste valorization, yet species-specific effects on microbial communities and biosafety remain unclear. Here, we compared the impacts of the earthworm Eisenia andrei (Ea) and the mealworm Tenebrio molitor (Tm) on [...] Read more.
The use of invertebrates for sewage sludge bioconversion offers a sustainable strategy for waste valorization, yet species-specific effects on microbial communities and biosafety remain unclear. Here, we compared the impacts of the earthworm Eisenia andrei (Ea) and the mealworm Tenebrio molitor (Tm) on the bacteriomes and mycobiomes of sewage sludge (ss) using 16S rRNA and ITS amplicon sequencing. Gut passage in both Ea and Tm markedly altered bacterial and fungal composition relative to ss, but produced distinct community profiles with differential shifts across multiple taxa. Both invertebrates reduced bacterial richness by ~40%, while fungal responses diverged: Ea largely preserved mycobiome richness despite reduced evenness, whereas Tm caused a near-complete collapse (~83% Amplicon Sequence Variant loss). Beta diversity analyses revealed clear, non-overlapping separation among ss, Ea, and Tm for both microbial domains. Tm frass showed strong enrichment of clinically relevant bacterial pathogens, while Ea casts exhibited no such enrichment. For fungi, Ea reshaped pathogen composition, whereas Tm largely eliminated fungal pathogens through broad community collapse. Both treatments reduced predicted antibiotic resistance gene abundance, but functional profiles differed, with Ea showing greater functional stability. These findings demonstrate that microbiome restructuring during bioconversion is species-dependent, with contrasting ecological and biosafety implications for downstream environmental use. Full article
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15 pages, 9315 KB  
Article
Sarcocystis spp. Investigations in Iberian Wild Caprinae Reveal a Remarkable Degree of Interconnection with Parasites’ Domestic Epidemiological Life Cycles
by Guillermo E. Delgado-De las Cuevas, Eglė Rudaitytė-Lukošienė, Petras Prakas, Josep Estruch, Roser Velarde, Antonio I. Plasencia-Gutiérrez, María L. García-Gil, Miguel Á. Habela and Rafael Calero-Bernal
Pathogens 2026, 15(8), 816; https://doi.org/10.3390/pathogens15080816 - 1 Aug 2026
Viewed by 194
Abstract
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 [...] Read more.
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
(This article belongs to the Section Parasitic Pathogens)
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28 pages, 17981 KB  
Article
Linking Host Provenance, Microbial Assembly, and Environmental Legacy Effects in the Root-Associated Microbiome of Tripterygium wilfordii Hook f.
by Dongdong Ma, Shuzhen He, Shaoying Li, Li Lin, Yihui Wang, Lei Feng, Zhaoshou Lin, Chengzhen Wu and Ping Song
Microorganisms 2026, 14(8), 1694; https://doi.org/10.3390/microorganisms14081694 - 1 Aug 2026
Viewed by 256
Abstract
Plant-associated microbiomes play critical roles in regulating plant growth, nutrient acquisition, and stress adaptation. However, whether geographically distinct plant provenances retain heritable signatures that influence microbiome assembly under uniform environmental conditions remains poorly understood. In this study, 16S rRNA amplicon sequencing was employed [...] Read more.
Plant-associated microbiomes play critical roles in regulating plant growth, nutrient acquisition, and stress adaptation. However, whether geographically distinct plant provenances retain heritable signatures that influence microbiome assembly under uniform environmental conditions remains poorly understood. In this study, 16S rRNA amplicon sequencing was employed to characterize root-associated bacterial communities of clonally propagated Tripterygium wilfordii derived from nine provenances and cultivated under identical soil conditions, with additional sampling from native populations. Host provenance significantly affected community composition, explaining 27.0% and 32.6% of the variation in rhizosphere and endophytic communities, respectively. Rhizosphere bacterial diversity differed significantly among provenances, whereas endophytic communities showed stronger differentiation in community structure and deterministic host selection. Although native plants exhibited lower bacterial diversity, they recruited more potential plant growth-promoting bacteria compared with transplanted plants. Environmental factors, particularly historical mean annual precipitation and longitude of native habitats, significantly influenced community diversity and structure. Distance–decay patterns demonstrated that root-associated bacterial communities retained climatic imprints from their native provenances despite cultivation under common-garden conditions. This study provides evidence that plant provenance can leave persistent microbial signatures and highlights the importance of integrating host genetic background and microbiome characteristics to understand ecological adaptation and improve germplasm utilization in medicinal plants. Full article
(This article belongs to the Section Plant Microbe Interactions)
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19 pages, 3728 KB  
Article
Long-Term Pepper (Capsicum annuum L.) Monoculture Reshapes Rhizosphere Soil Chemistry, Microbiota, and Metabolite Profiles
by Fan Yang, Zihang Han, Ying Zhang, Xin Wang, Yuting Hong, Xiaoke Chang, Wenrui Yang, Yaxian Zhao and Qiuju Yao
Agriculture 2026, 16(15), 1663; https://doi.org/10.3390/agriculture16151663 - 1 Aug 2026
Viewed by 168
Abstract
Continuous monoculture alters rhizosphere soil conditions and microbial community structure, but the integrated soil biochemical, microbial, and metabolomic responses of pepper (Capsicum annuum L.) rhizosphere soils remain insufficiently characterized. Here, we compared uncropped/non-continuously cropped pepper soil (Y0) with soil under 10 years [...] Read more.
Continuous monoculture alters rhizosphere soil conditions and microbial community structure, but the integrated soil biochemical, microbial, and metabolomic responses of pepper (Capsicum annuum L.) rhizosphere soils remain insufficiently characterized. Here, we compared uncropped/non-continuously cropped pepper soil (Y0) with soil under 10 years of pepper monoculture (Y10) using soil physicochemical assays, enzyme measurements, 16S rRNA and ITS amplicon sequencing, untargeted UHPLC-Q Exactive HFX metabolomics, and predictive functional profiling. Long-term monoculture markedly separated Y10 from Y0 in multivariate analyses. Y10 soils showed higher organic matter, available nitrogen, available phosphorus, available potassium, and electrical conductivity in soil-water extracts, whereas microbial biomass carbon and pH were lower. Soil enzyme profiles also differed between treatments. Microbial alpha diversity declined under Y10, and bacterial and fungal community structures were clearly separated between treatments. At the taxonomic level, Acidobacteriota and several oligotrophic bacterial taxa were relatively enriched in Y0, whereas Proteobacteria, Bacteroidota, Chloroflexi, Bacillota, Pseudomonas, Bacillus, and several fungal genus-level taxa increased in Y10. Untargeted metabolomics revealed extensive remodeling of rhizosphere metabolites, with 413 up-regulated and 21 down-regulated differential metabolites in Y10. Differential metabolites were mainly associated with carboxylic acids and derivatives, benzene and substituted derivatives, fatty acyls, aromatic-compound transformation, sulfur metabolism, alkaloid biosynthesis, and microbial metabolism. Correlation analyses further linked key microbial taxa with soil pH, microbial biomass carbon, available nutrients, electrical conductivity, and enzyme activities. These results indicate that long-term pepper monoculture is associated with coordinated shifts in soil chemical status, microbial community composition, and metabolite profiles. The study provides an integrated basis for understanding rhizosphere changes under pepper continuous-cropping systems while recognizing that functional predictions and metabolite annotations require experimental validation. Full article
(This article belongs to the Special Issue Soil Management and Interdisciplinary Approaches to Global Challenges)
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19 pages, 6728 KB  
Article
Possible Role of Gut Microbiota in Polypropylene Microplastics-Induced Immunity and Reproductive Dysfunction in Mice
by Di Xu, Yunqi Liu and Deli Xu
Toxics 2026, 14(8), 679; https://doi.org/10.3390/toxics14080679 - 31 Jul 2026
Viewed by 125
Abstract
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 [...] Read more.
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
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15 pages, 1628 KB  
Article
A Gap in the Prairie Nitrogen Cycle: Nitrogen Fixation Is Low, Despite Presence of Diverse Nitrogen Fixing Bacteria
by Bikram K. Das, Amrit Koirala and Volker S. Brözel
Nitrogen 2026, 7(3), 79; https://doi.org/10.3390/nitrogen7030079 - 30 Jul 2026
Viewed by 284
Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Nitrogen–Carbon Interactions in Global Biogeochemistry)
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27 pages, 3207 KB  
Article
Divergent Gut Microbiota Configurations Are Associated with Contrasting Physiological Profiles in Grazing Yaks and Introduced Feedlot Holstein Cattle Under High-Altitude Conditions
by Ding Li, Haozheng Li, Shu Zhang, Tong Wu, Dongyang Ye and Yaping Jin
Microorganisms 2026, 14(8), 1647; https://doi.org/10.3390/microorganisms14081647 - 28 Jul 2026
Viewed by 201
Abstract
The Qinghai–Tibet Plateau presents extreme environmental challenges, including hypobaric hypoxia and nutritional scarcity, to which indigenous yaks (Bos grunniens) are remarkably adapted, whereas introduced Holstein cattle (Bos taurus) often exhibit severe maladaptation. This study compared the gut microbiota of [...] Read more.
The Qinghai–Tibet Plateau presents extreme environmental challenges, including hypobaric hypoxia and nutritional scarcity, to which indigenous yaks (Bos grunniens) are remarkably adapted, whereas introduced Holstein cattle (Bos taurus) often exhibit severe maladaptation. This study compared the gut microbiota of grazing yaks (n = 20) and feedlot Holstein cattle (n = 20) under high-altitude conditions using 16S rRNA gene amplicon sequencing (for community composition) and shotgun metagenomic sequencing (for direct functional profiling of CAZy, COG, and KEGG pathways), combined with in vitro fermentation, digestive enzyme assays, and serum immune- and growth-related indicators. Results: The yak gut microbiota was dominated by Proteobacteria (35 ± 4%) and Actinobacteria (15 ± 2%), whereas Holstein cattle were dominated by Firmicutes (40 ± 4%) and Bacteroidetes (25 ± 3%). At the species level, NR-based metagenomic annotation suggested that Acinetobacter-related taxa, putatively assigned as Acinetobacter pseudolwoffii and A. lwoffii, were abundant in yaks. Functional profiling revealed that the yak microbiota was enriched in CAZy families CE1, GT2, and GT4, whereas the feedlot Holstein cattle microbiota showed enrichment of several KEGG orthologs related to multidrug efflux and carbohydrate transport, including dinF/mepA/vmrA and susC/susD. In vitro fermentation using enriched culturable fecal bacterial consortia showed higher dry matter digestibility and digestive enzyme activities in yak-derived consortia than in Holstein-derived consortia. For serum immune indicators, IgG was significantly higher in feedlot Holstein cattle, whereas IgA and IgM did not differ significantly between groups. Yaks showed higher serum levels of TNF-α, IL-6, TGF-β1, IL-4, IL-10, and IL-13, but lower IL-1β. Conclusions: These findings indicate that divergent gut microbiota configurations are associated with contrasting physiological profiles (e.g., digestive and immune functions) in grazing yaks and introduced feedlot Holstein cattle under the same high-altitude environment. However, due to the confounding effects of diet and management system, causal relationships cannot be inferred from this comparative study. Full article
(This article belongs to the Section Gut Microbiota)
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11 pages, 6562 KB  
Communication
Extreme Dominance of Coxiella-like Endosymbionts Reveals a Highly Simplified Microbiota in Argas persicus from Mexico
by Juan Carlos Herrera-Salazar, Cristina García-De la Peña, Abigail Rivera-Torres, Annely Zamudio-López, Sergio I. Barraza-Guerrero and Quetzaly K. Siller-Rodríguez
Arthropoda 2026, 4(3), 12; https://doi.org/10.3390/arthropoda4030012 - 28 Jul 2026
Viewed by 140
Abstract
Ticks of the family Argasidae are nidicolous ectoparasites of considerable ecological and veterinary importance because of their role as reservoirs and vectors of microorganisms. Despite the wide distribution of Argas persicus, information on its associated bacterial microbiome remains limited, particularly in the [...] Read more.
Ticks of the family Argasidae are nidicolous ectoparasites of considerable ecological and veterinary importance because of their role as reservoirs and vectors of microorganisms. Despite the wide distribution of Argas persicus, information on its associated bacterial microbiome remains limited, particularly in the Americas, and little is known about populations inhabiting livestock-associated peridomestic environments. In this study, we characterized the bacterial microbiota associated with A. persicus from a semi-arid region of northern Mexico using 16S rRNA gene (V3–V4) amplicon sequencing. Ticks were collected from cracks and crevices in wooden structures within a small rustic goat farm, illustrating the ability of this nidicolous species to persist in sheltered livestock-associated environments beyond its traditional association with poultry. Ten pools of internal soft tissues were analyzed. The bacterial community exhibited a highly simplified structure dominated by Proteobacteria (99.69%), particularly Coxiella-like endosymbionts (92.63%). Secondary taxa, including Arsenophonus (6.30%), together with Pseudomonas, Acinetobacter, and Sphingomonas, were detected at low relative abundances. Independent sequence comparisons against the NCBI and EMBL-EBI databases supported a conservative interpretation of the dominant lineage as Coxiella-like endosymbionts rather than confirmed Coxiella burnetii. These findings provide the first characterization of the bacterial microbiome associated with A. persicus in Mexico and suggest that populations inhabiting rustic livestock environments can harbor highly simplified bacterial communities dominated by symbiotic bacteria. Full article
(This article belongs to the Topic Ticks and Tick-Borne Pathogens: 2nd Edition)
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23 pages, 7798 KB  
Article
Interindividual Variability in Raffinose Fermentation by Human Gut Microbiota and Metabolomic Signature of a High-Efficiency In Vitro Degrader, Limosilactobacillus reuteri subsp. reuteri
by Wei Dai, Min Quan, Guangli Yu and Qingsen Shang
Foods 2026, 15(15), 2649; https://doi.org/10.3390/foods15152649 - 28 Jul 2026
Viewed by 263
Abstract
Background/Objectives: Raffinose is a prebiotic trisaccharide fermented by human gut microbiota, yet the strain-level determinants of its degradation and associated metabolic outputs remain poorly characterized. Methods: In the present study, anaerobic fermentation, 16S rRNA gene amplicon high-throughput sequencing, culturomics, and metabolomics [...] Read more.
Background/Objectives: Raffinose is a prebiotic trisaccharide fermented by human gut microbiota, yet the strain-level determinants of its degradation and associated metabolic outputs remain poorly characterized. Methods: In the present study, anaerobic fermentation, 16S rRNA gene amplicon high-throughput sequencing, culturomics, and metabolomics were conducted to address this question. Results: In vitro fermentation of raffinose was performed using fecal samples from 16 healthy donors, and substantial interindividual variation was observed in substrate consumption, microbiota composition, and short-chain fatty acid production. Through culturomics, 204 bacterial strains spanning 18 species were isolated, among which Limosilactobacillus reuteri subsp. reuteri exhibited the highest raffinose-degrading efficiency. Untargeted metabolomics comparing L. reuteri subsp. reuteri cultured on raffinose versus glucose revealed a distinct metabolic shift, with 290 metabolites significantly upregulated, including the putatively identified fructooligosaccharide 1-kestose—a compound with documented prebiotic and anti-inflammatory properties. KEGG enrichment further highlighted coordinated remodeling of nucleotide and amino acid metabolism. Conclusions: Collectively, this study provides a strain-level framework for understanding how raffinose shapes the gut microbiota and identifies L. reuteri subsp. reuteri as a key metabolic hub linking prebiotic consumption to the production of bioactive metabolites. Full article
(This article belongs to the Section Food Nutrition)
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23 pages, 2113 KB  
Article
How Complex Dietary Fibers Can Be Used to Shape the Human Gut Microbiome Toward Reduced Inflammatory Potential: A Pilot Study
by Maria Luisa Savo Sardaro, Sahana Kuthyar, Omolola Dada, Nimra Deivassagayame, Michael Tran, Ryder Kern, Sophie Koenig, Yosef Seidman, Matteo Atallah and Katherine R. Amato
Molecules 2026, 31(15), 2613; https://doi.org/10.3390/molecules31152613 - 27 Jul 2026
Viewed by 376
Abstract
Microbiome-linked pathologies in humans have significantly increased over recent decades, suggesting that lifestyle changes, particularly those related to diet, have contributed to the disruption of beneficial microbial composition and functions. Specifically, modern processed diets that are low in dietary fiber and high in [...] Read more.
Microbiome-linked pathologies in humans have significantly increased over recent decades, suggesting that lifestyle changes, particularly those related to diet, have contributed to the disruption of beneficial microbial composition and functions. Specifically, modern processed diets that are low in dietary fiber and high in fat and sugar can lead to the depletion of bacterial taxa over generations and contribute to chronic inflammatory diseases. These pathologies can potentially be prevented by increasing fiber intake, making the promotion of dietary fiber crucial for human health. Despite the recognized importance of fiber integration, there remains a significant gap in the understanding of the use of multiple dietary fibers in food to promote microbiota diversity, as well as which dietary fibers promote specific microbial taxa to restore symbiosis. To address this gap, we conducted an in vitro fermentation study using fecal samples from two individuals. We tested three types of dietary fibers of varying complexity: inulin, pectin, and dextran in a β-glucan–based medium. Samples were collected over a 48 h fermentation period (0–4–8–24–32–48 h) to evaluate temporal shifts in microbial composition and short-chain fatty acid (SCFA) production. Through 16S rRNA gene amplicon sequencing, we found that the introduction of different fibers steered the microbiota of both individuals toward a convergent trajectory by 24–48 h. This result indicated that fiber complexity can reduce inter-individual variation in microbial community structure. Distinct levels of polysaccharide complexity between fiber types modulated specific bacterial taxa, supporting the concept that consuming a diversity of dietary fiber acts on complementary microbial niches. Notably, the observed shifts toward butyrate-associated taxa and reduction of pro-inflammatory lineages with dextran/β-glucan are relevant for pathologies characterized by dysbiosis, such as inflammatory bowel disease (IBD). Together, these results underscore the value of incorporating multiple fibers into food production, including fermented foods, to enhance prebiotic properties, stimulate the growth of fiber-fermenting bacteria, and promote microbial diversity. While these observations derive from a controlled in vitro pilot setting, they support the concept that multi-fiber dietary strategies based on complementary fermentable fibers with prebiotic properties may help shift the microbiome away from a pro-inflammatory state. Accordingly, dietary guidelines and public health approaches aimed at reducing chronic disease risk may benefit from emphasizing the inclusion of composite fiber blends rather than relying solely on single-fiber supplementation. Full article
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14 pages, 8093 KB  
Article
Characterization of blaNDM-1 and blaOXA-23-Type Carbapenemases in Acinetobacter baumannii Isolated from Post-Surgical Patients
by Sana Gul, Nawab Ali, Muhammad Qasim, Maali Alahmad, Muhammad Saeed Khan, Zull E. Nourain, Sadir Zaman, Yar Muhammad and Waheed Ullah
Antibiotics 2026, 15(8), 722; https://doi.org/10.3390/antibiotics15080722 - 24 Jul 2026
Viewed by 289
Abstract
Background: Acinetobacter baumannii is an important opportunistic pathogen responsible for healthcare-associated infections, particularly among critically ill, intensive care unit (ICU), and post-surgical patients. The emergence of carbapenem-resistant A. baumannii (CRAB) has become a major therapeutic challenge worldwide because of its multidrug-resistant nature [...] Read more.
Background: Acinetobacter baumannii is an important opportunistic pathogen responsible for healthcare-associated infections, particularly among critically ill, intensive care unit (ICU), and post-surgical patients. The emergence of carbapenem-resistant A. baumannii (CRAB) has become a major therapeutic challenge worldwide because of its multidrug-resistant nature and limited treatment options. Despite the increasing prevalence of CRAB in Pakistan, information regarding the molecular characterization of carbapenem resistance genes among isolates recovered from surgical site infections (SSIs) remains limited. Methods: A cross-sectional study was conducted from November 2023 to February 2024 at Khalifa Gul Nawaz Hospital, Bannu, Khyber Pakhtunkhwa, Pakistan. A total of (n = 118) surgical wound specimens were collected from patients with clinically diagnosed SSIs. A. baumannii isolates were identified using standard biochemical tests and confirmed by 16S rRNA gene sequencing. In vitro antimicrobial susceptibility was determined by Kirby–Bauer disk diffusion according to CLSI 2024 guidelines. In addition, the concentration-dependent inhibition-zone response of imipenem and meropenem against carbapenem-resistant isolates was evaluated using an agar well diffusion assay. Molecular detection of blaNDM-1 and blaOXA-23 was performed by polymerase chain reaction (PCR), and representative amplicons were subjected to Sanger sequencing for further analysis. Results: In the current study, the total number of (n = 118) wound specimens from healthcare-associated patients were processed, in which A. baumannii-positive isolates (n = 23, 19.5%) were documented. Its prevalence was higher in males (69.6%) compared to females, and was strongly associated (78.2%) with elderly patients (aged 51–68 years). In vitro susceptibility testing revealed that 91.3% of isolates harbored multidrug-resistant (MDR) attributes. Antimicrobial susceptibility profiling revealed high levels of multidrug resistance, with 82.6% of isolates resistant to imipenem and meropenem, as well as 100% resistance to aztreonam and gentamicin. Colistin showed the highest activity, with 87.0% of isolates remaining susceptible. In the agar well diffusion assay, measurable inhibition of the carbapenem-resistant isolates by imipenem and meropenem occurred only at higher concentrations. Molecular screening of resistance genes identified blaOXA-23 in 60.9% and blaNDM-1 in 30.4% of isolates. Co-expression of both genes was detected in some (n = 4) isolates. Among the selected MDR isolates included in the gene resistance analysis, imipenem and meropenem resistance were recorded in 9/14 blaOXA-23-positive isolates and 5/7 blaNDM-1-positive isolates. Conclusions: This study substantiates an escalated incidence of carbapenem-resistant, MDR A. baumannii in post-surgical infections. blaOXA-23 were documented as the predominant carbapenemase gene, with co-expression of blaNDM-1 in a substantial proportion of isolates. These findings provide an important phenotypic and molecular characterization of selected carbapenemase genes in healthcare-associated infections, highlighting the exigency for strengthened antimicrobial stewardship and infection control strategies in the hospitals of the region. Full article
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20 pages, 10724 KB  
Article
Sediment Bacteria and Driving Factors in Intertidal Flats and Vegetated Zones of Mangrove Ecosystems in the Northern Beibu Gulf During Summer
by Jiaodi Zhou, Peng He, Zhijun Dai, Dongliang Lu, Bin Yang, Hu Huang, Zeyu Wang, Solomon Felix Dan and Wen Song
Water 2026, 18(14), 1762; https://doi.org/10.3390/w18141762 - 21 Jul 2026
Viewed by 271
Abstract
Mangrove sediments harbor complex bacterial communities that play critical roles in ecosystem functioning. In this study, we investigated the spatial patterns and environmental drivers of sediment bacterial communities across intertidal flats and vegetated zones in five representative mangrove habitats spanning the Northern Beibu [...] Read more.
Mangrove sediments harbor complex bacterial communities that play critical roles in ecosystem functioning. In this study, we investigated the spatial patterns and environmental drivers of sediment bacterial communities across intertidal flats and vegetated zones in five representative mangrove habitats spanning the Northern Beibu Gulf, South China. Utilizing high-throughput 16S rRNA gene amplicon sequencing, we analyzed bacterial composition and diversity from sediments collected in Qinzhou, Fangchenggang, and Beihai. Results indicated that bacterial communities were dominated by Proteobacteria (37–45%), followed by Bacteroidota and Acidobacteriota; however, a considerable proportion of taxa remained unclassified, particularly in intertidal flats. Bacterial richness and diversity were generally higher in vegetated zones, where sediments were more acidic and nutrient-rich, whereas intertidal sediments were more alkaline and contained higher chlorophyll-a (Chl-a) concentrations. Beta-diversity analysis revealed distinct differences in community structures between zones and regions, which were shaped by both deterministic environmental filtering and stochastic processes. Redundancy analysis (RDA) indicated that bacterial communities assembly driven by niche differentiation influences salinity (Sal), pH, biogenic silica (BSi), total phosphorus (TP), and total nitrogen (TN), as these factors vary across sites due to differing environmental filtering intensities. These findings highlight the distinct differences in mangrove sediment bacterial communities between intertidal flats and vegetated zones, which are shaped by local sediment physicochemical conditions and regional environmental gradients. They provide critical insights for the conservation and restoration of mangrove ecosystems. Full article
(This article belongs to the Special Issue Advances in Biogeochemistry of Estuaries)
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15 pages, 12340 KB  
Article
Watercress Extract Reduces Experimental Colitis by Modulating Inflammation and Regulating the Gut Microbiota
by Guangyi Shen, Dekun Cheng, Jathya C. Karunathilaka, Jieun Woo, Donglu Li, Jonica L. Wooton, Patricia Jaynes, Tingting Ju and Weicang Wang
Nutrients 2026, 18(14), 2369; https://doi.org/10.3390/nu18142369 - 20 Jul 2026
Viewed by 398
Abstract
Background/Objectives: Watercress (Nasturtium officinale), a cruciferous vegetable rich in phenethyl isothiocyanate (PEITC) and bioactive phytochemicals, has demonstrated anti-inflammatory and cytoprotective activities in multiple disease models; however, its effects on colitis remain insufficiently characterized. In the present study, we investigated the effects [...] Read more.
Background/Objectives: Watercress (Nasturtium officinale), a cruciferous vegetable rich in phenethyl isothiocyanate (PEITC) and bioactive phytochemicals, has demonstrated anti-inflammatory and cytoprotective activities in multiple disease models; however, its effects on colitis remain insufficiently characterized. In the present study, we investigated the effects of watercress extract supplementation in dextran sulfate sodium (DSS)-induced experimental colitis. Methods: Male C57BL/6 mice were fed either a standard AIN-93G diet or a diet supplemented with 0.5% (w/w) watercress extract for 4 weeks, followed by DSS administration to induce acute colitis. Colonic histopathological injury, immune responses, barrier integrity, and gut microbiota composition were evaluated. In addition, the activity of PEITC, a major bioactive constituent of watercress, was examined in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages in vitro. Results: Watercress extract attenuated DSS-induced colon shortening and reduced histopathological injury. The supplementation of watercress extract also decreased colonic immune cell accumulation, suppressed the expression of pro-inflammatory mediators, and preserved intestinal barrier integrity. The 16S rRNA gene amplicon sequencing further revealed that watercress extract reshaped gut microbial composition, including increased abundance of Monoglobus and Adlercreutzia, and reduced abundance of microbial taxa such as Enterococcus and Enterorhabdus. Moreover, PEITC suppressed LPS-induced inflammatory activation in RAW264.7 macrophages by reducing nitric oxide production, inhibiting p38 MAPK phosphorylation, and downregulating multiple inflammatory cytokines and chemokines. Conclusions: These findings demonstrate that watercress extract alleviates experimental colitis through attenuating mucosal inflammation, preserving intestinal barrier function, and modulating the gut microbiota, highlighting watercress as a promising dietary strategy for improving gut health and mitigating intestinal inflammation. Full article
(This article belongs to the Special Issue Food Intake and Inflammatory Bowel Disease)
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