Search Results (242)

The striped stem borer Chilo suppressalis (Lepidoptera: Crambidae) is one of the most serious pests of water bamboo Zizania latifolia. Microbiota dynamics across the life cycle of C. suppressalis are a prerequisite for comprehending the symbiotic relationship between C. suppressalis and its microbiota. In this study, we characterized the structural features of the gut and ovary, as well as the associated microbiota of C. suppressalis. The gut is anatomically divided into the foregut, midgut and hindgut. Notable structural and ultrastructural differences were observed between adults and larvae, the details of which have not been previously documented. Microbial sequencing of gut, ovary, and egg samples revealed variations in relative sequence abundances among these tissues. At the phylum level, Proteobacteria and Firmicutes were the predominant groups. At the family level, Bacillaceae, Enterobacteriaceae, Enterococcaceae, Halomonadaceae, Moraxellaceae, and Streptococcaceae were detected in the gut, ovary, and egg, albeit with different relative sequence abundances. The larval midgut exhibited the highest bacteria diversity among all samples examined. The compositional distribution of bacterial genera varied considerably across developmental stages, diet, and gut compartment, and some genera were identified as core microbial taxa. These findings provide a descriptive account of the microbial community structure associated with different tissues and life stages of C. suppressalis. They also provided important insights into the investigation of insect–bacteria symbioses, thereby facilitating effective biocontrol of this species. Full article

The escalating global threat of antimicrobial resistance (AMR) has intensified efforts to identify safe, effective, and sustainable alternatives to in-feed antibiotics in livestock production. The bovine gastrointestinal microbiome plays a central role in host immunity, nutrient utilization, and disease resilience, positioning microbiome-modulating interventions as promising candidates for antimicrobial stewardship. Despite growing experimental interest, a systematic synthesis of the available evidence in cattle is lacking. This systematic review aimed to evaluate the efficacy of microbiome-modulating interventions, including probiotics, prebiotics, postbiotics, phytogenic feed additives, essential oils, organic acids, and native rumen microbial supplements, as strategies to reduce antimicrobial use in cattle, and to characterize their effects on gut microbial diversity, fermentation characteristics, and host health and performance outcomes. A systematic search of Scopus, Web of Science, and EBSCOhost (including Academic Search Ultimate, MEDLINE with full text, and CAB Abstracts with Full text) was conducted in accordance with PRISMA guidelines. Studies were eligible if they used cattle (dairy cattle, beef cattle, calves, or mixed production systems), employed a microbiome-modulating intervention, and reported at least one microbiological or host outcome. Seventeen peer-reviewed studies published between 2010 and 2025 were included after full-text screening. Risk of bias was assessed using an adapted SYRCLE tool, which identified moderate overall study quality; the majority of included studies were randomized controlled trials or controlled experiments, though reporting of allocation concealment and blinding was inconsistent across studies. Across the 17 included studies, five broad categories of interventions were evaluated: probiotics (n = 5 studies), prebiotics (n = 2), postbiotics and organic acids (n = 4), phytogenic additives and essential oils (n = 4), and native rumen microbial supplements (n = 2). Animals spanned neonatal dairy calves, weaned Holstein calves, dairy heifers, lactating dairy cows, and Bos indicus feedlot beef cattle. Probiotics and organic acids most consistently improved growth performance: benzoic acid supplementation increased average daily gain by 8.4% (p < 0.05) and fructo-oligosaccharide prebiotics elevated body weight at weaning by 6.7% (p < 0.01). Native rumen microbial supplements improved energy-corrected milk yield by up to 3.1% without increasing dry matter intake. Polyphenols and bile acids demonstrated the strongest immunological and disease-preventive effects, reducing calf mortality by approximately 40% and disease severity by approximately 35%, respectively. Microbiome analyses revealed intervention-dependent increases in microbial diversity and shifts toward taxa associated with improved fermentation efficiency, including enrichment of propionate-producing Prevotellaceae, butyrate-associated Ruminococcus, and hindgut Bifidobacterium. Rumen fermentation outcomes included reductions in the acetate:propionate ratio and ammonia-N concentrations and improvements in fiber digestibility of 3.6–4.4 percentage units in dairy cows. Phytogenic additives preserved microbial diversity without inducing broad-spectrum suppression, functioning primarily as microbiome stabilizers rather than direct antimicrobial replacements. This systematic review provides evidence that gut microbiome modulation may enhance growth performance, improve fermentation efficiency, and reduce disease susceptibility in cattle, thereby supporting antimicrobial use reduction across dairy, beef, and mixed production systems. Effect magnitudes varied substantially across intervention categories and production contexts, and study quality was moderate, underscoring the need for larger, pre-registered trials with standardized outcome reporting and direct antibiotic comparator arms. Probiotics, prebiotics, and bile acid metabolites showed the greatest potential as components of integrated antimicrobial stewardship strategies in cattle production. Full article

Breeding stallions are subjected to increased metabolic and physiological demands during the reproductive season, which may lead to enhanced production of reactive oxygen species and disruption of redox balance. The present study evaluated the effects of dietary antioxidant supplementation on oxidative status, metabolic profile, and hindgut fermentation in stallions undergoing intensive semen collection activity. Ten adult breeding stallions were assigned either to a control group or to a treatment group receiving a commercial antioxidant supplement (Oxyliver^®) for 60 days, followed by a 60-day post-supplementation period. Blood and fecal samples were collected at regular intervals to assess hematological, biochemical, oxidative, and fermentation parameters. Hematological and biochemical variables remained within physiological ranges throughout the study, with no significant treatment-related effects, indicating that the supplementation was safe and well-tolerated. In contrast, during the supplementation period, oxidative status was significantly influenced by the antioxidant treatment, as demonstrated by reduced lipid peroxidation and increased total antioxidant capacity (TAC) and ferric reducing antioxidant power (FRAP). These findings indicate an enhancement of systemic antioxidant defenses. In conclusion, dietary antioxidant supplementation effectively improved oxidative balance in breeding stallions without adversely affecting metabolic health, supporting its potential use as a nutritional strategy to mitigate oxidative stress associated with intensive reproductive activity. Full article

Cockroaches display a double symbiosis: an obligate intracellular one with Blattabacterium spp., and a complex extracellular non-vertically transmitted gut microbiota, that may be affected by horizontally transmitted factors. Four experiments using 16S rRNA gene amplicon sequencing were conducted to analyze the microbiota of the hindgut and feces of adult cockroaches. They aimed to understand the influence of the environment and feces on the acquisition and development of the hindgut microbiota. We observed that sample type (hindgut vs. feces), rearing conditions (environment, i.e., place and diet), coprophagy, and host influenced microbiota composition. Cockroaches initially germ-free, placed in non-sterile conditions and with blocked parental coprophagy, were unable to develop the normal microbiota of the control population, demonstrating that coprophagy is essential for acquiring a normal microbiota. This also showed that, in the absence of parental fecal input, the cockroach gut microbiota is strongly diminished. Moreover, when exploring fecal microbiota differences among three cockroach species, the greatest divergence was observed between Periplaneta americana and Blattella germanica, with Blatta orientalis occupying an intermediate position. Therefore, P. americana was selected for fecal transplantation on B. germanica. This transplantation experiment indicates that different species select different gut microbes, and that even when they receive feces from other species, only some of those bacteria are retained. Overall, these results suggest that beyond other factors, the host species had the strongest influence on shaping the cockroach gut microbiota. Full article

Locally sourced roughages constitute the dietary foundation of donkey production in northern China, yet their fermentation behavior in the donkey hindgut remains poorly characterized. The present study employed in vitro batch cultures to compare the dry matter disappearance (IVDMD), gas production (GP) kinetics and short-chain volatile fatty acid (VFA) profiles of five locally available feedstuffs—peanut vine (PNV), soybean straw (SBS), wheat shell (WS), reed grass (RG) and bamboo leaf (BL)—when incubated separately with cecal or colonic microbial inocula obtained from Dezhou donkeys. After 40 h incubation, both IVDMD and total VFA concentrations ranked identically across the two hindgut segments: PNV > SBS > WS > RG > BL (p < 0.05), and all indices were consistently higher in the cecal than in the colonic fermentation system (p < 0.05). The asymptotic gas production (A) and the time required to reach half of A (T₁/₂) followed the same ranking as IVDMD (p < 0.01), indicating that feedstuffs with greater fermentable substrate availability sustained fermentation for longer periods. In contrast, the fractional gas production rate (c) and the average gas production rate (AGPR) in RG and BL exceeded those of PNV, SBS, and WS under cecal incubation (p < 0.05), reflecting rapid utilization of a small pool of readily fermentable components in these fibrous substrates. Regarding VFA stoichiometry, BL yielded the highest molar proportion of acetate and PNV the lowest in the colonic system (p < 0.05), whereas the propionate proportion followed the order PNV > SBS > WS > RG > BL (p < 0.01). Consequently, the acetate-to-propionate (A:P) ratio and the non-glucogenic-to-glucogenic (NGR) ratio were highest in BL (p < 0.05). The molar proportions of butyrate and branched-chain VFAs (BCVFAs) in WS, RG, and BL were greater than those in PNV (p < 0.05). Collectively, the five feedstuffs differed markedly in their fermentability, kinetic behavior, and VFA yield profiles, reflecting distinct energy-supply potentials for the donkey host. PNV and SBS exhibited superior overall in vitro fermentation performance and are therefore recommended as preferred roughage sources, whereas BL and RG may serve complementary roles by supporting hindgut epithelial health through elevated butyrate production. These findings provide a mechanistic basis for the rational selection and combination of locally sourced roughages to optimize feeding strategies and improve feed-use efficiency in donkey production. Full article

Background/Objectives: Gastrojejunal–ileal interposition with bipartition and sleeve gastrectomy (GJIB-SG) is a novel metabolic procedure developed to combine functional foregut exclusion with hindgut stimulation while preserving duodenal continuity and endoscopic biliary access. This study evaluated the medium-term glycemic, weight-loss, and nutritional safety outcomes of GJIB-SG in patients with obesity and long-standing type 2 diabetes (T2D). Methods: A retrospective single-center cohort of 30 consecutive patients with obesity and T2D who underwent GJIB-SG between January 2016 and August 2019 and reached at least 60 months of postoperative follow-up was analyzed at baseline and at 12, 24, 36, 48, and 60 months. Longitudinal data were analyzed by repeated-measures ANOVA with Greenhouse–Geisser correction and Bonferroni-adjusted pairwise comparisons. Diabetes remission was classified using the 2021 American Diabetes Association consensus definition (A1C < 6.5%, medication-free). Results: Mean body weight decreased from 102.4 ± 13.6 kg preoperatively to 73.5 ± 7.6 kg at 60 months (p < 0.001; mean %TWL 27.4%, mean %EWL 99.4%). Mean A1C decreased from 9.4 ± 1.6% to 6.0 ± 1.4% at 60 months (p < 0.001). Complete medication-free remission was achieved by 70.0% of patients at 12 months and 44.8% at 60 months; cumulatively, 25 of 30 (83.3%) achieved complete remission at one or more intervals, and 3 patients (10.0%) never achieved A1C < 6.5%. Triglycerides, total cholesterol, and LDL cholesterol decreased by 56%, 39%, and 35%, respectively. No protein–energy malnutrition or hypoalbuminemia occurred; however, a late rise in parathyroid hormone and a return of 25-OH vitamin D toward preoperative insufficient values by 60 months indicate the need for sustained micronutrient surveillance. One cardiovascular death at 24 months was not considered procedure related. Conclusions: In this single-center cohort, GJIB-SG was associated with durable weight loss, sustained glycemic improvement with cumulative complete remission in 83.3% of patients, and absence of severe nutritional complications over 60 months. Prospective comparative studies with longitudinal mixed-effects analysis are warranted to define the role of GJIB-SG within the metabolic–surgical armamentarium. Full article

Coprophagy, the ingestion of feces, is widespread among vertebrates and plays an important role in hindgut-fermenting herbivores by facilitating nutrient recycling and maintaining gut microbial stability. However, most studies have focused on cecal or fecal microbiota, with limited attention to microbial communities at other body sites. Here, we used Brandt’s vole, a species exhibiting frequent coprophagic behavior, to examine how coprophagy prevention affects hindgut fermentation and microbial communities across multiple sites, including the tongue, lung, stomach, and cecum. Coprophagy prevention increased food intake but reduced body weight gain and significantly decreased cecal acetate, propionate, and butyrate concentrations. At the microbial level, coprophagy prevention increased the Simpson index of the tongue microbiota and induced modest compositional shifts in the tongue, lung, and stomach microbiota. In contrast, the cecal microbiota exhibited greater compositional and predicted functional changes. Notably, coprophagy prevention reduced the Bray–Curtis distance between tongue and cecal microbiota without altering the number of shared amplicon sequence variants. Together, these findings indicate that coprophagy not only promotes efficient nutrient recycling through hindgut fermentation but may also influence microbiota composition across behaviorally interconnected digestive niches. Full article

Gastrointestinal microbiota are essential for fiber degradation, energy metabolism, nutrient utilization, and environmental adaptation in ruminants. Although sika deer and reindeer both belong to the family Cervidae, they differ in ecology, feeding habits, and digestive physiology, which may be reflected in their gastrointestinal microbiota. Here, we used 16S rRNA amplicon sequencing to characterize the gastrointestinal microbial communities of healthy 5-year-old male sika deer and reindeer, with particular attention to taxonomic composition, diversity patterns, and predicted functional profiles across anatomical segments. Both species were dominated by a limited number of highly abundant taxa, but clear interspecific differences were observed. At the phylum level, Bacillota and Bacteroidota predominated in both species, whereas Methanobacteriota was more abundant in reindeer and Bacillota was relatively more abundant in sika deer. At the genus level, methanogen-associated taxa were more prominent in reindeer, whereas Bacteroides, Prevotellaceae, and fiber-degradation-related taxa were more abundant in sika deer. Distinct segment-specific microbial patterns were observed along the gastrointestinal tract, especially among the foregut, small intestine, and hindgut. Alpha diversity varied across segments, whereas beta diversity showed clear separation among segments. Functional prediction indicated differences mainly in the overall structure of predicted functional profiles rather than in individual pathways. These findings provide baseline information for understanding gastrointestinal microecology and adaptive mechanisms in cervids. Full article

Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures. Full article

This study aimed to investigate the effects of dietary bile acids (BA) supplementation on serum antioxidant capacity, fecal fermentation characteristics, microbial diversity, and community composition in culled ewes. Twenty 5-year-old culled Hu ewes with similar body weights (42.95 ± 1.07 kg) were randomly allocated to two groups (n = 10 per group). The control group (CON) received a basal diet, while the treatment group (BA400) was fed the same basal diet supplemented with 400 mg/kg BA. Compared with the CON group, the BA400 group showed enhanced serum activities of total antioxidant capacity, superoxide dismutase, and glutathione peroxidase, while also showing reduced concentrations of cortisol, malondialdehyde, and reactive oxygen species (p < 0.05). Fecal pH, ammonia nitrogen, total volatile fatty acids, and the concentrations and proportions of individual volatile fatty acids remained unaffected by BA supplementation (p > 0.05). Microbial analysis revealed that the BA400 group exhibited higher fecal bacterial richness and diversity than the CON group (p < 0.05). Analysis of similarities revealed significant differences between the CON and BA400 groups (R = 1.000, p = 0.007). Specifically, BA supplementation increased the relative abundances of beneficial taxa, including Verrucomicrobiota and Akkermansia, while decreasing potentially pathogenic bacteria such as Campylobacterota and Proteobacteria. These findings indicate that dietary BA supplementation improves serum antioxidant capacity and modulates fecal microbial diversity and community structure in culled ewes, suggesting that hindgut microbiota may contribute to the health benefits of BA supplementation in ruminant production. Full article

Diversifying forage sources may improve the sustainability and flexibility of dairy production. In a 60 d feeding trial, 72 mid-lactation Holstein cows were assigned to three treatments (24 cows/group) and fed a total mixed ration in which corn silage represented 41.16% of dietary dry matter in the control diet; 25% or 50% of this corn silage fraction was replaced with triticale silage (TS) on a dry matter basis. The study evaluated whether partial TS substitution could maintain lactational performance while affecting fecal fermentation and microbiota. Replacing corn silage with TS did not affect milk yield, 4% fat-corrected milk, major milk components, or metabolic indicators. However, 50% replacement increased fecal bacterial richness and diversity, as reflected by ACE, Chao1, and Shannon indices, and altered the overall microbial community structure. This treatment also changed fecal volatile fatty acid profiles, including increasing the proportions of branched-chain volatile fatty acids. Overall, TS can replace up to 50% of the corn silage fraction in the ration of mid-lactation cows without compromising milk production or composition, while modifying hindgut microbial ecology and fermentation patterns, thereby offering greater ration flexibility when corn silage availability is limited or costly. Full article

Growing Angus steers (n = 20) were blocked by weight and randomly assigned to one of two treatment groups: Control group (CON, n = 10) fed a feedlot ration ad libitum, or a ruminally protected hydrogenated fat-embedded calcium gluconate (HFCG) treatment group (HFCG, n = 10), which was fed the control ration top-dressed at 16 g/head/day for 55 days. During the slaughter process, digesta samples were collected from the cecum, colon, and rectum. Acetate concentrations were greater in the cecal and rectal digesta of steers (p ≤ 0.05) in the HFCG treatment group. Propionate concentrations were greater in the cecal, colonic, and rectal (p ≤ 0.05) digesta of steers in the HFCG treatment group. Butyrate concentrations were greater (p = 0.098) in the colon digesta of steers in the HFCG treatment group; however, they were not different in the cecal and rectal digesta. To determine the microbial composition within each section of the hindgut, DNA was extracted, and 16S rRNA gene sequencing was performed. Data were analyzed using a General Linear Model with dietary treatment as the main effect. Species richness in the cecum, colon, and rectum was not different between treatments. Erysipelotrichaceae, Peptostreptococcaceae, and Atopobiaceae abundances were increased (p ≤ 0.05) in the cecal bacterial community of steers in the HFCG group, while a significant decrease (p ≤ 0.05) in Rikenellaceae and Muribaculaceae abundances was recorded within the same bacterial community. In the colon bacterial community of steers in the HFCG group, Ruminococcaceae and Muribaculaceae abundances were elevated (p ≤ 0.05), while there was a reduction (p ≤ 0.05) in Lachnospiraceae, Erysipelotrichaceae, Atopobiaceae, and Peptostreptococcaceae abundances. Paeniclostridium, Romboutsia, and Turicibacter abundances were increased (p ≤ 0.05) in the cecal bacterial community of steers in the HFCG group, while there was a decrease (p ≤ 0.05) in Rikenellaceae_RC9 _gut_group abundance within the same bacterial community. In the colon microbiota of steers in the HFCG group, Turicibacter abundance was decreased (p ≤ 0.05). Supplementing growing steers with HFCG impacted some members of the bacterial populations, which have important roles in gut homeostasis and health, along with the formation of beneficial end-products in the gastrointestinal tract. Full article

In ruminant nutrition, the lignocellulosic complex is a primary constraint limiting the utilization of dietary fiber. The objective of this study was to evaluate the effects of inoculating lignin-degrading bacteria (LDB) isolated from the ruminant rectum on in vitro rumen fermentation characteristics. Rectal fecal samples were collected from healthy beef cattle, dairy cattle, buffaloes, and goats (n = 4 per species) using the grab sampling technique. Twenty-eight bacterial colonies were isolated through enrichment and screening on media containing sodium lignosulfonate. Lignin degradation efficiency was assessed spectrophotometrically, while laccase activity was determined using a 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) oxidation assay. Seven isolates exhibiting ligninolytic activity (1.4–5.6% degradation efficiency) were selected to evaluate their effects on in vitro rumen fermentation using a completely randomized design with four replicates. LDB treatments were standardized to a concentration of 2.4 × 10⁵ colony-forming units/mL of rumen fluid medium, while the control received an equal volume of a 0.85% sterile NaCl solution. A rice straw-based total mixed ration served as the substrate, with rumen fluid collected from beef cattle. All treatments were incubated for 48 h. Notably, isolate BC3 consistently enhanced in vitro dry matter digestibility (23.1%), total gas production (18.6%), and total volatile fatty acid concentrations (13.2%) relative to the control and other LDB isolates (p < 0.01). All seven LDB isolates were identified as Gram-negative, rod-shaped, facultative anaerobic bacteria that exhibit catalase activity and tolerate moderately acidic conditions. Phylogenetic tree analysis based on 16S rRNA gene sequencing identified isolate BC3 as being closely related to Escherichia coli strains. These findings demonstrate that the ruminant hindgut is a promising source of LDB with the functional potential to enhance feed digestibility and fermentation end-products in the rumen. Future research should prioritize in vivo trials to evaluate the safety and efficacy of LDB as a direct-fed microbial, specifically focusing on its impact on animal performance and health. Full article

Accurate and physiologically relevant in vitro models are needed to predict nutrient digestibility and hindgut fermentation in pigs, as conventional in vivo trials are resource-intensive and raise animal welfare concerns. This study evaluated and compared the predictive performance of three in vitro digestion approaches—shaking (S), dialysis (D), and a combined shaking plus dialysis (SD) method—for estimating in vivo apparent total tract digestibility (ATTD) and fermentation characteristics across weaning, growing, and finishing pigs. Commercial diets were subjected to simulated gastric and small-intestinal digestion using S, D, or SD, followed by fecal inoculation to model hindgut fermentation for 12 and 48 h. During the gastrointestinal phase, crude protein digestibility was highest with D (>75%), intermediate with SD, and lowest with S (50–60%), indicating that product removal by dialysis mitigated enzyme inhibition from metabolite accumulation. After 48 h of fermentation, all methods showed strong linear correlations with in vivo ATTD (r > 0.93), but only D achieved high absolute agreement (Lin’s CCC > 0.95 for dry matter and crude protein). Moreover, D and SD at 48 h closely reflected in vivo fecal profiles of skatole, indole, and microbial enzyme activities, with D at 12 h showing an especially strong correlation for protease (r = 0.98). While D provided the most precise predictions of absolute values, the SD method offered an optimal balance between physiological relevance and operational efficiency, supporting its use as a robust, high-throughput platform for porcine feed evaluation and fecal nitrogenous odorant prediction. Full article

Hybridization is pivotal for germplasm innovation, yet how reciprocal crossing regulates digestive characteristics in sub-cold-water fish remains unclear. This study systematically compared differences in intestinal morphology, physiological function, and microbial community assembly among herbivorous Schizothorax prenanti, carnivorous S. davidi, and their reciprocal hybrids using histological analysis, digestive enzyme assays, and 16S rRNA sequencing. Results indicated that parental intestinal characteristics were highly consistent with their feeding habits. Orthogonal hybrids exhibited a mosaic phenotype, combining the maternal muscular gut structure with high paternal-like lipase activity, and were characterized by an enrichment of the potential probiotic Lactococcus. In contrast, reciprocal hybrids presented a mismatch between morphology and function: despite developed hindgut folds, key digestive enzyme activities were low, and the gut microbiota was dominated by environmental bacteria such as Methylobacterium. Our findings indicate a spatially dependent assembly dynamic: the host genetic background strongly drives microbiome divergence in the anterior segments (foregut and midgut), whereas the long-term administration of a standardized diet ultimately promotes structural convergence in the hindgut. The orthogonal cross yielded a phenotype characterized by an apparent co-occurrence of specific host enzymes and distinct microbiota, suggesting an inferred physiological potential for lipid digestion that requires further multi-omics validation. These findings provide preliminary insights into the associations between genetic background and intestinal traits, providing a theoretical basis for the targeted breeding of Schizothorax species. Full article