Alterations in bile acid profile and pathways contribute to hepatic inflammation in cancer cachexia, a syndrome worsening the prognosis of cancer patients. As the gut microbiota impinges on host metabolism through bile acids, the current study aimed to explore the functional contribution of gut microbial dysbiosis to bile acid dysmetabolism and associated disorders in cancer cachexia. Using three mouse models of cancer cachexia (the C26, MC38 and HCT116 models), we evidenced a reduction in the hepatic levels of several secondary bile acids, mainly taurodeoxycholic (TDCA). This reduction in hepatic TDCA occurred before the appearance of cachexia. Longitudinal analysis of the gut microbiota pinpointed an ASV, identified as Xylanibacter rodentium, as a bacterium potentially involved in the reduced production of TDCA. Coherently, stable isotope-based experiments highlighted a robust decrease in the microbial 7α-dehydroxylation (7α-DH) activity with no changes in the bile salt hydrolase (BSH) activity in cachectic mice. This approach also highlighted a reduced microbial 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 12α-hydroxysteroid dehydrogenase (12α-HSDH) activities in these mice. The contribution of the lower production of TDCA to cancer cachexia was explored in vitro and in vivo. In vitro, TDCA prevented myotube atrophy, whereas in vivo hepatic whole transcriptome analysis revealed that TDCA administration to cachectic mice improved the unfolded protein response and cholesterol homeostasis pathways. Coherently, TDCA administration reversed hepatic cholesterol accumulation in these mice. Altogether, this work highlights the contribution of the gut microbiota to bile acid dysmetabolism and the therapeutic interest of the secondary bile acid TDCA for hepatic cholesterol homeostasis in the context of cancer cachexia. Such discovery may prove instrumental in the understanding of other metabolic diseases characterized by microbial dysbiosis. More broadly, our work demonstrates the interest and relevance of microbial activity measurements using stable isotopes, an approach currently underused in the microbiome field.

Maintenance hemodialysis (MHD) patients frequently exhibit immune dysregulation and gut dysbiosis, both of which contribute to increased infection risk and adverse outcomes. However, the relationship between gut microbial composition and immune competence in this population remains underexplored.

This study assessed 45 MHD patients and 30 healthy controls, stratifying MHD patients into immunocompetent (HD-NLI, CD4+/CD8+ ≥ 1) and immunodeficient (HD-LI, CD4+/CD8+ < 1) groups. Circulating cytokines (IL-6, IL-10, IL-12, TNF-α, IFN-γ) were quantified using ELISA. Gut microbiota profiles were derived via 16S rRNA gene sequencing (V3-V4 regions), followed by QIIME2 and LEfSe-based bioinformatics analyses.

HD-LI patients displayed severe T cell dysregulation and elevated pro-inflammatory cytokines. Compared to controls, HD patients had reduced abundance of beneficial taxa (e.g., Prevotella copri, Bacteroides vulgatus, Agathobacter), and enrichment of pro-inflammatory taxa (e.g., Escherichia-Shigella, Blautia, Citrobacter). LEfSe identified 39 discriminatory taxa with distinct immune group signatures. Redundancy analysis revealed that CD4+ levels, CD4+/CD8+ ratios, and TNF-α significantly shaped microbiota composition. Correlation analysis confirmed strong associations between immune parameters and microbial taxa involved in short-chain fatty acid (SCFA) metabolism.

This study provides novel evidence linking gut microbial dysbiosis to immune impairment in MHD patients. The findings suggest that SCFA-producing bacteria are depleted in immunodeficient states, offering a potential target for microbiota-directed immunomodulatory therapies in ESRD.

Metagenomic sequencing deepened our knowledge about the role of the intestinal microbiota in human health, and several studies with various methodologies explored its dynamics during antibiotic treatments. We compared the impact of four widely used antibiotics on the gut bacterial diversity. We used plasma and fecal samples collected during and after treatment from healthy volunteers assigned to a 5-day treatment either by ceftriaxone (1 g every 24 h through IV route), ceftazidime/avibactam (2 g/500 mg every 8 h through IV route), piperacillin/tazobactam (1 g/500 mg every 8 h through IV route) or moxifloxacin (400 mg every 24 h through oral route). Antibiotic concentrations were measured in plasma and feces, and bacterial diversity was assessed by the Shannon index from 16S rRNA gene profiling. The relationship between the evolutions of antibiotic fecal exposure and bacterial diversity was modeled using non-linear mixed effects models. We compared the impact of antibiotics on gut microbiota diversity by simulation, using various reconstructed pharmacodynamic indices. Piperacillin/tazobactam was characterized by the highest impact in terms of intensity of perturbation (maximal [IQR] loss of diversity of 27.3% [1.9; 40.0]), while moxifloxacin had the longest duration of perturbation, with a time to return to 95% of baseline value after the last administration of 13.2 d [8.3; 19.1]. Overall, moxifloxacin exhibited the highest global impact, followed by piperacillin/tazobactam, ceftazidime/avibactam and ceftriaxone. Their AUC between day 0 and day 42 of the change of diversity indices from day 0 were, respectively, -13.2 Shannon unit.day [-20.4; -7.9], -10.9 Shannon unit.day [-20.4; -0.6] and -10.1 Shannon unit.day [-18.3; -4.6]. We conclude that antibiotics alter the intestinal diversity to varying degrees, both within and between antibiotics families. Such studies are needed to help antibiotic stewardship in using the antibiotics with the lowest impact on the intestinal microbiota.

Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL-1) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.

Major depression (MD) significantly impacts individual well-being and society. The vagus nerve plays a pivotal role in the gut-brain axis, facilitating bidirectional communication between these systems. Recent meta-analyses suggest potential antidepressant effects of probiotics, although their mechanisms remain unclear. This study aimed to assess the impact of a multi-species probiotic (OMNi-BiOTiC® STRESS Repair) on vagus nerve function in 43 MD patients and 43 healthy controls (HC). Participants received either probiotics or placebo twice daily. Serum and stool samples were collected at baseline, 7 days, 28 days, and 3 months. Vagus nerve (VN) function was evaluated using 24-hour electrocardiography (ECG) for heart rate variability (HRV), alongside stool microbiome analysis via 16S rRNA sequencing. After 3 months, MD patients receiving probiotics demonstrated significantly improved morning VN function compared to HC. MD participants who were in the probiotic group showed a significant increase in Christensellales, particularly Akkermansia muciniphila along with improved sleep parameters (use of sleep medication, sleep latency) as measured by the Pittsburgh Sleep Quality Inventory (PSI). This study highlights potential physiological benefits of probiotics in MD, potentially mediated through VN stimulation. Understanding these mechanisms could lead to novel therapeutic approaches for MD management.

Despite extensive investigations into the microbiome and metabolome changes associated with colon polyps and colorectal cancer (CRC), the microbiome and metabolome profiles of individuals with colonic polyposis, including those with (Gene-pos) and without (Gene-neg) a known genetic driver, remain comparatively unexplored. Using colon biopsies, polyps, and stool from patients with Gene-pos adenomatous polyposis (N = 9), Gene-neg adenomatous polyposis (N = 18), and serrated polyposis syndrome (SPS, N = 11), we demonstrated through 16S rRNA sequencing that the mucosa-associated microbiota in individuals with colonic polyposis is representative of the microbiota associated with small polyps, and that both Gene-pos and SPS cohorts exhibit differential microbiota populations relative to Gene-neg polyposis cohorts. Furthermore, we used these differential microbiota taxa to perform linear discriminant analysis to differentiate Gene-neg subjects from Gene-pos and from SPS subjects with an accuracy of 89% and 93% respectively. Stool metabolites were quantified via 1H NMR, revealing an increase in alanine in SPS subjects relative to non-polyposis subjects, and Partial Least Squares Discriminant Analysis (PLS-DA) analysis indicated that the proportion of leucine to tyrosine in fecal samples may be predictive of SPS. Use of these microbial and metabolomic signatures may allow for better diagnostric and risk-stratification tools for colonic polyposis patients and their families as well as promote development of microbiome-targeted approaches for polyp prevention.

This study aims to analyze the different therapeutic responses between topical antimicrobial-corticosteroid combination and topical corticosteroids alone on improving the skin microbiome and skin barrier of patients with atopic dermatitis (AD).

Forty patients with mild-to-moderate AD were randomly assigned to receive two kinds of treatment. Skin swabs were collected from the lesional sites and nearby nonlesional sites at baseline, after topical medication treatment and 2 weeks post-treatment, and were analyzed by DNA sequencing of the fungal internal transcribed spacer (ITS)1-5 rDNA gene and the V3V4 region of the bacterial 16S rRNA gene.

According to our research analysis, both topical steroids alone and combination treatment of steroids and antimicrobials effectively improved the severity of AD and repaired skin barrier. AD lesions were characterized by a decreased sebum level, lower abundance of Cutibacterium and a higher abundance of Staphylococcus. A combined topical treatment with an antimicrobial and steroid showed better responses in increasing skin sebum level and restoring the skin bacterial microbiome, whereas topical steroid alone did not improve skin dysbiosis.

A combined therapy with antimicrobial and steroid helps to recover the skin microbiome. Further studies are necessary to explore the therapeutic effects of treatments aiming at balancing the microbiome.

Excess amino acids from a protein-rich diet are mainly catabolized in the liver. However, it is still unclear to what extent the gut microbiota may be involved in the mechanisms governing this catabolism. Therefore, the aim of this study was to investigate whether consumption of different dietary protein concentrations induces changes in the taxonomy of the gut microbiota, which may contribute to the regulation of hepatic amino acid catabolism. Consumption of a high-protein diet caused overexpression of HIF-1α in the colon and increase in mitochondrial activity, creating a more anaerobic environment that was associated with changes in the taxonomy of the gut microbiota promoting an increase in the synthesis of secondary bile acids, increased secretion of pancreatic glucagon. This effect was demonstrated in pancreatic islets, where secondary bile acids stimulated the expression of the PC2 enzyme that promotes glucagon formation. The increase in circulating glucagon was associated with an induction of the expression of hepatic amino acid-degrading enzymes, an effect attenuated by antibiotics. Thus, high protein intake in mice and humans induced the increase of different species in the gut microbiota with the capacity to produce secondary bile acids leading to an increase in secondary bile acids and glucagon levels, promoting amino acid catabolism.

The problem of soil polycyclic aromatic hydrocarbon (PAH) pollution in coking plant sites has been widely studied in recent years, but there is a lack of research on the correlation between soil microorganisms, soil metabolomics, and soil properties. Thus, in this study, the long-term impact of coke combustion on soil microbial community structure, enzyme activities, and metabolic pathways within a former coking plant site was investigated. Soil samples were collected from both the coking production area (CA group) and office area (OLA group), approximately 0 to 20 cm in depth. Compared with OLA group, elevated levels of 16 PAHs in the list of US EPA were detected by gas chromatography-mass spectrometry in the CA group. Several dominant microorganisms, such as Altererythrobacter, Lysobacter, and Sulfurifustis, were identified by 16 s ribosomal DNA sequencing in the CA group. The fatty acid biosynthesis pathway exhibited specific inhibition, while the phenylalanine metabolic pathway was promoted in response to PAH stress. Long-term PAH exposure led to the inhibition of soil urease activity. The co-occurrence network of microorganisms revealed intricate patterns of co-metabolism and co-adaptation within complex bacterial communities, facilitating their adaptation to and decomposition of soil-borne PAHs. This research could provide valuable insights into the community characteristics and metabolic mechanisms of microorganisms inhabiting PAH-polluted soil within coking plant sites. The findings enhance our understanding of the indigenous soil microbiome and its intricate network dynamics under the persistent stress of PAHs, contributing to a more comprehensive knowledge of soil ecosystems in such environments.

The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.

The complexity of soil microplastic pollution has driven deeper exploration of waste management strategies to evaluate environmental impact. This study introduced oversized microplastics (OMPs, 1-5 mm) during membrane composting to produce organic fertilizers, and conducted a 2 × 2 pot experiment: exogenous OMPs were added when normal fertilizer (no OMPs intervention) was applied, while artificial removal of OMPs was implemented when contaminated fertilizer (with OMPs) was used. The study assessed the effects of these management strategies on lettuce growth, soil environments, and potential biological safety risks related to the spread and expression of high-risk antibiotic resistance genes (ARGs) in humans. Results showed that both exogenous OMPs addition and removal negatively affected plant height and harvest index, with shifts in the rhizosphere microbial community identified as a key factor rather than soil nutrients. Exogenous OMPs altered rhizosphere and endophytic microbial communities, and plant growth-promoting bacteria were transferred to the surface of OMPs from rhizosphere soil. In contrast, bacteria such as Truepera, Pseudomonas, and Streptomyces in compost-derived OMPs supported lettuce growth, and their removal negated these effects. Some endophytic bacteria may promote growth but pose public health risks when transmitted through the food chain. OMPs in composting or planting significantly enhanced the expression of target ARGs in lettuce, particularly blaTEM. However, simulated digestion results indicated that OMPs reduced the expression of six key ARGs, including blaTEM, among the ten critical target ARGs identified in this context. Notably, the removal management strategies raised five of them posing potential risks from lettuce consumption. This study highlights that both introducing and removing OMPs may pose ecological and food safety risks, emphasizing the need for optimized organic waste management strategies to mitigate potential health hazards.

Disinfectants are non-antibiotic biocides that have been used extensively in daily life, particularly since the onset of the COVID-19 pandemic. However, their effect on drug resistance has not received sufficient attention. Here, marine medaka were subjected to an environmental concentration (10 μg/L) of benzalkonium chloride (BAC), sulfamethazine (SMZ), and their combination, aiming to elucidate their contributions to antibiotic resistance. Overall, 10 μg/L BAC exhibited a stronger induction potential for multiple antibiotic resistance genes (ARGs) relative to a similar level of SMZ. Specifically, tetracycline resistance genes were readily induced, regardless of exposure to BAC, SMZ, or their combination. BAC exhibited a more pronounced induction of ARGs than SMZ and showed a stronger potential to stimulate multidrug resistance. SMZ and BAC induced distinct virulence factors. Bacteria increased pathogenicity primarily through biofilm formation and enhanced community sensing under SMZ exposure, whereas iron acquisition and the production of reactive oxygen species appeared to be the main mechanisms by which bacteria evaded host defenses under BAC exposure. A greater number of ARGs demonstrated a significant positive correlation with virulence factors following BAC exposure compared to both the SMZ exposure group and the co-exposure group, which further confirmed the strong ability of BAC to induce multidrug resistance. In summary, owing to the typically unregulated and low-dose use of disinfectants in daily life and their pseudo-persistence in the environment, their potential to induce resistance may exceed that of antibiotics. Therefore, increased attention and preventive measures are required to address their resistance-inducing effects.

Biodesulfurization is crucial for sustainable biogas purification from hydrogen sulfide (H2S). This study investigates the operational limits of anoxic biotrickling filters (BTFs) for treating biogas with high H2S concentrations (up to 20,000 ppmv) using nitrite, along with simulated interruptions in H2S supply. The BTF achieved a maximum elimination capacity of 312 g S-H2S m-3 h-1 with an H2S removal efficiency of 98 % at an empty bed residence time of 284 s. A proportional-integral-derivative (PID) feedback control system was successfully employed to maintain an H2S outlet concentration close to the requisite setpoint (100 and 500 ppmv) by adjusting the nitrite flow rate, thereby minimizing its accumulation. Continuous nitrite feeding after interruptions in H2S supply was essential to avoid H2S release due to sulfate-reducing bacteria. Multi-omics analyses, combining metagenomics and proteomics, revealed Sulfurimonas as the dominant sulfur-oxidizing bacteria, which downregulates most enzyme genes involved in nitrogen and sulfur metabolism in response to substrate starvation. These findings underscore the resilience of BTFs under extreme conditions and the value of multi-omics approaches in understanding microbial population dynamics, positioning BTFs as a robust solution for large-scale biogas purification.

Apple replant disease (ARD) causes significant economic losses globally, including in China. Analyzing the causes of this replant disease from the perspective of rhizosphere microecology is therefore essential. In this study, we examined rhizosphere soils from apple trees subjected to continuous cropping. The mechanisms underlying ARD were elucidated through high-throughput sequencing of the soil microbiome, co-occurrence network analysis using NetShift, and correlation analyses. Core bacterial microbes were isolated, and their roles in altering the microecological environment were verified through reinoculation experiments. The results indicated that the disease indices for apple seedlings cultivated increased in continuously cropped soils. Bacterial diversity decreased in continuously cropped apple orchards for 10 years (R10) and 15 years (R15), but the relative abundance of Pseudomonas increased. In contrast, fungal diversity increased, with the relative abundance of Fusarium also increasing. As a dominant genus, Pseudomonas exhibited significant network variation after 10 years of consecutive cultivation, suggesting that this microorganism may play a key role in the occurrence of ARD. Moreover, the correlation analysis revealed, for the first time, that Pseudomonas is negatively correlated with bacterial diversity but positively correlated with the relative abundance of Fusarium, indicating a close relationship between Pseudomonas and Fusarium in continuously cropped soil. Four key Pseudomonas amplicon sequence variants (ASVs) strains were isolated from the continuously cropped rhizosphere soil of apple trees, and reinoculation experiments verified that introducing Pseudomonas exacerbated the occurrence of replant diseases in both strawberry and apple, with significantly higher disease indices compared to single Fusarium inoculation. The findings of this study provide new and timely insights into the mechanism underlying the occurrence of ARD.

The Tibetan Plateau is a high-altitude environment characterized by hypoxic conditions, strong ultraviolet rays, and significant temperature variations that affect the well-being of local residents, including mother-infant dyads. Adaptive evolution through lifestyle and dietary patterns plays an important role in nutrition during the maternal lactation period, which offers unique merits for investigation at the intersection of environmental and nutritional fields. Specifically, changes in the nutrient composition of human milk among Tibetan lactating mothers and their associated consequences for infants provide insight into early nutrition research and infant food production. In this study, the concentrations of vitamins A, D, E, and β-carotene in the human milk of Tibetan mothers, as well as the fecal microbiome profiles of their infants, were analyzed within the first month postnatal. The results showed that the fat-soluble vitamins in Tibetan human milk were at satisfactory levels, particularly during the colostrum stage, which may be attributed to the advantages of their dietary pattern and dwelling environment. Dynamic changes in the gut microbiota composition of Tibetan infants were observed, with the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria being relatively abundant. The abundance of Bifidobacterium increased as infants aged within the first month postnatal. Correlations were found between the fat-soluble vitamin composition in human milk and the characteristics of the infant gut microbiota, including alpha (α)-diversity indices and microbial abundances. These findings will help enhance the understanding of early nutrition under harsh natural conditions and will guide relevant innovations and improvements in the maternal and infant food industry.

Macroalgal blooms have frequently occurred in coastal waters, and a large amount of algogenic dissolved organic matter (DOM) is input into seawater as macroalgae degraded. It undergoes continuous changes under microbial degradation; however, the impact of microbially-modified marine DOM on the environmental behaviour of organic pollutants remains underexplored. This study focused on Ulva prolifera, the dominant species in green tides, and investigated the molecular diversity of DOM from U. prolifera degradation over a 100-day period and the role of DOM at different time points in the adsorption of organophosphate flame retardants onto goethite. Our findings revealed that dissolved organic carbon (DOC) in seawater increased sharply during the first two weeks, followed by a rapid decline, and eventually reached a stable level within 100 days. Multi-spectrum analysis and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), along with the results of spectral analysis, indicated an increase in the humification and aromaticity of DOM, accompanied by the transformation of protein components, suggesting a decrease in DOM bioavailability. Microbial abundance aligned with DOC trends, and 16S rRNA results revealed significant shifts in the microbial community during DOM transformation. A strong correlation between fluorescent DOM groups and microbial diversity was observed, and co-occurrence network analysis further identified Alteromonas and Vibrio as major contributors to DOM chemical diversity. The introduction of U. prolifera DOM reduced available surface sites on goethite, inhibiting the adsorption rate of tributyl phosphate (TnBP) in batch sorption experiments. However, this competitive sorption effect was mitigated by co-sorption, as DOM could bind with TnBP, explaining the observed increase in adsorption capacity. Redundancy analysis and verification tests suggested protein-like DOM components play a crucial role in sorption, and microbial transformation of DOM-proteins could diminish this effect. These findings underscore the importance of macroalgal DOM in influencing the environmental behaviour of organic pollutants and could supply a supplement about the ecological effect about macroalgal blooms.

Members of Dehalococcoides mccartyi (Dhc) are strictly anaerobic and play crucial roles in the restoration of many industrial sites impacted by chlorinated solvents, such as tetrachloroethene (PCE) and trichloroethene (TCE). In situ bioremediation with Dhc involves intricate procedures intended to minimize oxygen intrusion, and achieving optimal dechlorination performance in aquifers near the dense non-aqueous phase liquids source zone is challenging. Here, we respectively embedded Dhc strain 195 and the biomass of a Dhc-containing, PCE-dechlorinating consortium in poly(vinyl alcohol)-alginate hydrogel beads. The ethene-forming potential was well-retained in immobilized Dhc following a prolonged oxygen exposure spanning from 12 hours to 7 days, with dechlorination rates ranging from 54.6 ± 4.2-101.9 ± 13.5 µM Cl- released day-1. In contrast, suspended strain 195 and the Dhc-containing biomass exposed to oxygen for a shorter duration were completely deactivated, or suffered a substantial reduction in dechlorination potential. Cell immobilization also significantly improved the ability of Dhc to tolerate the toxic effects of chlorinated solvents. When exposed to 300 mg L-1 TCE or free-phase PCE, an immobilized Dhc inoculum enabled more rapid recovery of dechlorination activity with shorter lag phases and up to 2.1-fold higher dechlorination rate compared to the use of their suspended counterparts. Our results demonstrate the effectiveness of cell immobilization for shielding Dhc from various environmental stresses (e.g., oxygen exposure).

Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.

Compacted bentonite is one of the most promising engineered barrier materials used in Deep Geological Repositories (DGR) of high-level radioactive waste encapsulated in metal canisters. Determining bentonite compaction density threshold for bacterial presence and activity has been a long-standing objective, due to their implications for canisters' durability and, therefore, in the safety performance of DGR. This study provided new insights into the effect of dry density (1.5 and 1.7 g cm⁻³), acetate amendment, and long-term incubation (5 years) on the bentonite mineralogy as well as their bacterial community distribution and survival. Through Illumina sequencing, we demonstrated that higher dry density reduces the bacterial diversity with spore-forming bacteria such as Nocardioides, and Promicromonospora being predominant. Interestingly, Paracoccus and Pseudomonas were enriched in acetate-treated samples, suggesting the utilization of this carbon source and, consequently, supporting their viability and survival. In addition, spore-forming (e.g., Bacillus) and desiccation-resistant (e.g., Arthrobacter) microorganisms were isolated. X-ray diffraction and scanning electron microscopy analyses showed the stability of bentonite while indicating the probable formation of iron sulfides. These findings confirm the influence of bentonite compaction degree and long-term incubation on microbial viability and activity, highlighting their potential impact on the integrity and safety of future DGR.

There is currently increased interest in nanocellulose as a food emulsifier and dietary supplement. It was hypothesized that nanocellulose could modulate behaviors and glucose homeostasis in female mice using mechanisms of altered gut microbiome and immune modulation. An initial experiment was conducted with the objective of examining whether three common types of nanocellulose affected the gut microbiome of female C57BL/6 mice on a Western diet. Cellulose nanofibrils (CNF), TEMPO-CNF and cellulose nanocrystals were administered at the physiologically relevant dose of 30 mg/kg/day for 30 days by gavage, with cellulose and water groups as the positive and negative controls, respectively. Findings suggested that CNF had the strongest effect on the gut microbiome. CNF was therefore selected for a chronic 6-month study on the gut microbiome, immune system and behaviors in female NOD mice, a model for type 1 diabetes. Gut microbiome analysis suggested that there might be some beneficial changes following subchronic exposure (e.g., at the two-month timepoint), however, this effect was no longer seen after chronic consumption (e.g., at the six-month timepoint). CNF treatment also altered the immune homeostasis, including decreases in the splenic Mac-3+ population and serum level of proinflammatory chemokine LIX. Additionally, CNF consumption decreased diabetic incidences but had no effect on the depressive-like behavior and grip strength. However, further analysis, e.g., the insulin tolerance test, indicated that CNF-treated NOD mice might exhibit signs of insulin resistance. Taken together, nanocellulose dysregulated glucose homeostasis in female mice on a Western diet involving mechanisms related to alteration of the gut microbiome.

Auricularia auricula-judae is a widely cultivated mushroom species known for its edible and medicinal properties. Polysaccharides have been the focus of research because of their potential bioactivities; nonetheless, the structural complexity and molecular weight have hindered a complete understanding of their bioactivities. In this study, AP-1 polysaccharide was isolated from A. auricula-judae and subjected to ultrasonic degradation at different time points to improve their anti-inflammatory effects. The results showed that when AP-1 was degraded for 9 min (AP-2) and 20 min (AP-3), the NO inhibition rate was significantly increased in LPS-stimulated RAW 264.7 cells. The structural and physiochemical properties of native and degraded polysaccharides were analyzed, and it was found that the degradation process significantly reduced molecular weight and altered the particle size, viscosity, crystallinity, and helical structure. Furthermore, native and degraded polysaccharides (AP-1, AP-2, and AP-3) anti-inflammatory effects were investigated in the DSS-induced colitis mouse model. Degraded polysaccharides resulted in significant improvements, including recovery from weight loss, reduced disease activity, shortened colon length, and decreased inflammation, while AP-3 showed the most promising effects. Gut microbiota 16S rRNA sequencing revealed that AP-3 potentially increases healthy gut microbiota and inhibits unhealthy gut microbiota. Overall, this study demonstrates that ultrasonic degradation could be a great technique to modify polysaccharides' MW and physiochemical properties to improve anti-inflammatory and gut microbiota regulatory effects.

Probiotic microbes such as Lactobacillus may reduce serum total cholesterol (TC) and low-density lipoprotein (LDL) cholesterol. The objective of this study was to assess the effect of Lactobacillus plantarum strains CECT7527, CECT7528, and CECT7529 (LP) on the serum lipids, cardiovascular parameters, and fecal gut microbiota composition in patients with mild hypercholesterolemia. A randomized, double-blinded, placebo-controlled clinical trial with 86 healthy adult participants with untreated elevated LDL cholesterol ≥ 160 mg/dl was conducted. Participants were randomly allocated to either placebo or LP (1.2 × 109 CFU/d) for 12 weeks. LDL, HDL, TC, and triglycerides (TG), cardiovascular parameters (blood pressure, arterial stiffness), and fecal gut microbiota composition (16S rRNA gene sequencing) were assessed at baseline and after 12 weeks. Both groups were comparable regarding age, sex, and LDL-C at baseline. LDL-C decreased (mean decrease - 6.6 mg/dl ±  - 14.0 mg/dl, Ptime*group = 0.006) in the LP group but not in the placebo group. No effects were observed on HDL, TG, or cardiovascular parameters or overall gut microbiota composition. Responders to LP intervention (> 5% LDL-C reduction) were characterized by higher BMI, pronounced TC reduction, higher abundance of fecal Roseburia, and lower abundance of Oscillibacter. In conclusion, 12 weeks of L. plantarum intake moderately reduced LDL-C and TC as compared to placebo. LDL-C-lowering efficacy of L. plantarum strains may potentially be dependent on individual difference in the gut microbiota. Trial registration: DRKS00020384, dated 07/01/2020.

Microplastics pose serious risks for aquatic organisms such as fishes, shrimps and bivalves. Bivalves are particularly vulnerable due to their filter-feeding strategy and sedentary life. While the microplastic bioaccumulation in bivalves has been well documented, the effects of microplastics accumulation on bivalve's gut microbiome in tropical sea waters remains poorly understood. To fill this knowledge gap, a 10-day feeding experiment with 13 mg L-1 polyethylene terephthalate particles was conducted using three commercially important bivalve species: Anadara cornea, Geloina expansa, and Meretrix meretrix taken from two contrasting locations (brackish water in protected Setiu Wetlands compared to open water in Kertih River) to investigate the effect of microplastic pollution on diversity and composition of gut prokaryotes using 16S rRNA amplicon sequencing. The results showed that alpha diversity of gut prokaryotes differed among species after microplastic exposure. For example, microplastic exposure increased operational taxonomic units (OTUs) richness of gut prokaryotes in G. expansa compared to A. cornea and M. meretrix during 10-day treatment. Community structure of prokaryotic community in bivalves gut showed strong divergence between Setiu Wetlands and Kertih River. Significant effects of microplastic exposure on relative abundance of prokaryotic phyla were also observed. Gut microbiome of G. expansa showed increase of relative abundance of Archaea and Firmicutes after microplastic exposure. The results suggest that microplastic treatment promotes dominance of certain bacterial species, likely those with plastic-metabolizing capabilities, potentially boosting bivalve resilience to microplastic contamination.

Metalloenzyme cofactors and oxygen conditions are crucial for microbial metabolism, yet their combined effects on microbial ecosystems remain unexplored. This study explores the impact of micronutrient amendments (Zn, Fe, Co and their combinations) on the microbial community composition in oxygenated (73 m) and deoxygenated (200 m) waters of the Arabian Sea. Through controlled microcosm experiment and 16S rRNA amplicon sequencing, we observed that micronutrients significantly alter nutrient concentrations and microbial dynamics. At 73 m, micronutrient treatments reduced nitrate, nitrite and ammonia levels, whereas at 200 m, they increased nitrate and silicate levels. Total bacterial counts (TBCs) were higher in all treatments at both depths, with Fe showing the highest counts. Alpha diversity indicated that Fe-amended flask increased microbial diversity the most at 73 m, while mixed treatments had a pronounced effect at 200 m. Taxonomic analysis revealed significant genus-level variations in both bacteria and archaea. One-way analysis of variance (ANOVA) confirmed micronutrient impacts on nutrients and TBC. Canonical correspondence analysis (CCA) and non-metric multidimensional scaling (NMDS) revealed distinct clustering based on oxygen conditions. These results confirm our hypothesis that micronutrient amendments in varying oxygen levels distinctly alter microbial community composition and nutrient cycling in marine environments.

The pathobiome is a comprehensive biotic environment that includes a community of all disease-causing organisms within the plant, defining their mutual interactions and the resultant effects on plant health. The concept and understanding of alfalfa pathobiome and its impact on host fitness in natural ecosystems remain largely unexplored. We have previously reported on the diverse composition of the alfalfa pathobiome in the field production environment. In this study, using modern transcriptomics tools combined with computational analyses, we applied a novel 'field host genomics' approach to survey gene expression changes in visually healthy and diseased plants collected from commercial alfalfa fields. As a result of this work, genes and pathways involved in alfalfa responses to a diverse field pathobiome were identified and the genetic basis of the crop's resistance to multi-pathogenic infections was proposed. In addition to offering genetic insights into host resistance to multi-pathogenic infections in natural ecosystems, this strategy can facilitate identification of plants with tolerant genotypes adapted to field pathobiome, followed by their application in alfalfa breeding programs.

Synthesizing the microbial community with a high denitrifying capacity is the key for achieving efficient removal of nitrogen species in wastewater treatment plants. Here, we integrated the evolutionary top-down enrichment and bottom-up bioaugmentation to construct a high-efficiency Pseudomonas-recruited denitrifying consortium (PRDC). A PRDC with a high specific denitrification rate of 109.49 ± 10.58 mg N/(g MLVSS·h) was enriched after 181 days of microbiota construction with pre-inoculation of Pseudomonas strain onto carriers. The 16S rRNA gene sequencing analysis suggested that the pre-inoculated Pseudomonas was quickly washed out and replaced by dominant denitrifying genera, such as Halomonas and Thauera, under different hydraulic retention times (HRTs). The pre-inoculated Pseudomonas can facilitate PRDC by providing public goods, but compromising its nutrient requirements. The dominant community assembly processes switched from homogeneous selection to ecological drift and dispersal limitation under shortened HRT. Furthermore, a shortened HRT facilitated the colonization of new immigrants and intensified their competition with the pre-existing dominant denitrifiers. The PRDC carriers achieved a 1.65-fold enhancement in sludge denitrification and reduced the corresponding chemical oxygen demand consumption at a carrier filling ratio of 30%. Overall, our study developed a novel technique using Pseudomonas aeruginosa as a trigger to enrich high-efficiency denitrifying consortia for wastewater treatment.

Preventing oral microbiome dysbiosis is crucial for averting the onset and progression of periodontal diseases. Phellodendron bark extract (PBE) and its active component berberine exhibit antibacterial properties against periodontal pathogenic bacteria. Although they inhibit Porphyromonas gingivalis (P. gingivalis)-induced dysbiosis in vitro in multiple species of saliva-derived planktonic cultures, their effects on microcosm biofilm models remain unclear. In this study, we aimed to elucidate the dysbiosis-suppressive effects of PBE and berberine chloride (BC) on biofilm formation.

PBE or BC was added during the formation of in vitro microcosm biofilms containing saliva and P. gingivalis, which were anaerobically cultured for one week. Next-generation sequencing was performed to assess microbiota composition, while quantitative real-time PCR was used to measure bacterial concentrations. Additionally, the butyrate concentration in the culture supernatant was assessed as biofilm pathogenicity.

PBE and BC treatments reduced the relative abundance of periodontal pathogenic bacteria, including P. gingivalis, and significantly increased the relative abundance of the genus Streptococcus and nitrate-reducing bacteria, including the genera of Neisseria and Haemophilus. Moreover, the treatment groups exhibited significantly decreased butyrate concentrations.

Our findings suggest that PBE and BC could suppress dysbiosis triggered by P. gingivalis in microcosm biofilms in vitro by decreasing the relative abundance and amount of periodontal pathogenic bacteria and enhancing those of nitrate-reducing bacteria that have a high relative abundance in orally healthy individuals. In summary, PBE and BC may contribute to the prevention of periodontal disease through their dysbiosis-suppressive and anti-inflammatory effects.

Fermented dairy products are known for their efficiency in delivering and protecting probiotic microorganisms. However, there is a growing demand for diversification of the market with plant-based products. The aim of this study was to develop an oat beverage enriched with inulin and fermented with Lacticaseibacillus rhamnosus LR B and evaluate its synbiotic effects in vitro. For this purpose, the validated dynamic colon model (the TNO Intestinal Model TIM-2) was used with focus on the composition of the gut microbiota and its production of metabolites to evaluate the functionality. The fermentation kinetics, sugars, organic acids and inulin dosage in the fermented oat beverage were also evaluated. The acidification rate was 16.91 10-3 pH units.min-1, reaching the final pH of 4.5 in 2.38 ± 0.05 h. Dosages of sucrose, glucose and lactic acid were 23.35 ± 0.45 g.L-1, 21.37 ± 0.77 g.L-1, 0.94 ± 0.05 g.L-1, respectively. After simulated in vitro digestion, the inulin concentration was partially preserved with 20.11 ± 0.21 maltose equivalent (μg.mL-1). The fermented and pre-digested oat beverage (with 7.71 ± 0.44 log CFU.mL-1) was fed into TIM-2, which was previously inoculated with feces from healthy adults. The analysis identified nine bacterial taxa that were significantly modulated compared to the standard ileal effluent medium (SIEM) control. An increase in relative abundance of Lactobacillus and Catenibacterium, and reduction in Citrobacter, Escherichia-Shigella, and Klebsiella was observed. In addition, the cumulative means of short-chain fatty acids (SCFAs) increased, especially for acetate and butyrate. These findings suggest that the developed oat beverage can positively influence the gut microbiota and its activity, highlighting possible health benefits.

Macrobrachium rosenbergii (giant freshwater prawn; GFP) holds considerable importance in aquaculture due to its high market demand and economic significance. Female GFP growth varies significantly, however, the processes responsible for these growth disparities remain unknown. In this study, intestinal and hemolymph samples of large (FL), medium (FM), and small (FS) female GFPs were collected to investigate the molecular mechanism of female GFP growth. Through the utilization of 16S rRNA sequencing and liquid chromatography-mass spectrometry metabolomics, significant intestinal flora and metabolites linked to the growth performance of female GFPs were identified. The dominant phyla of the three groups were the same, namely Firmicutes and Proteobacteria. Among groups, small females exhibited the lowest abundance of Proteobacteria (27.26 %) and the highest abundance of Firmicutes (70.10 %). The most abundant genus in each group was Lactococcus. Liquid chromatography-mass spectrometry identified 115 annotated differential metabolites, and essential metabolites related to female GFP growth performance were screened. The concentration of serum metabolites in the larger females exhibited a statistically significant variance compared to that of the smaller females. Through association analysis, we identified key genes, metabolites, and gut microbiota that influence the growth of female GFPs. Likewise, we used multi-omics techniques to establish two relationship models ("gut microbiota-GFP phenotype-metabolite", "gut microbiota-GFP phenotype-transcript"), and three important network association models ("DN5520_c0_g1-CW1-Bacteroides", "DN537746_c0_g1-BW-Roseburia" and "Picolinic acid-phenotype-Roseburia") were further developed. The present study provides novel insights into the mechanisms underlying the variability in individual growth among female GFPs. Our findings offer valuable information for future investigations exploring the correlation between gut flora and host organisms in aquatic environments.

Faecalibacterium prausnitzii is one of the most dominant commensal bacteria in the human gut, and certain anti-inflammatory functions have been attributed to a single microbial anti-inflammatory molecule (MAM). Simultaneously, substantial diversity among F. prausnitzii strains is acknowledged, emphasizing the need for strain-level functional studies aimed at developing innovative probiotics. Here, two distinct F. prausnitzii strains, KBL1026 and KBL1027, were isolated from Korean donors, exhibiting notable differences in the relative abundance of F. prausnitzii. Both strains were identified as the core Faecalibacterium amplicon sequence variant (ASV) within the healthy Korean cohort, and their MAM sequences showed a high similarity of 98.6%. However, when a single strain was introduced to mice with dextran sulfate sodium (DSS)-induced colitis, KBL1027 showed the most significant ameliorative effects, including alleviation of colonic inflammation and restoration of gut microbial dysbiosis. Moreover, the supernatant from KBL1027 elevated the secretion of IL-10 cytokine more than that of KBL1026 in mouse bone marrow-derived macrophage (BMDM) cells, suggesting that the strain-specific, anti-inflammatory efficacy of KBL1027 might involve effector compounds other than MAM. Through analysis of the Faecalibacterium pan-genome and comparative genomics, strain-specific functions related to extracellular polysaccharide biosynthesis were identified in KBL1027, which could contribute to the observed morphological disparities. Collectively, our findings highlight the strain-specific, anti-inflammatory functions of F. prausnitzii, even within the same core ASV, emphasizing the influence of their human origin.

The present study investigated the richness and diversity of vaginal microbiota among a cohort of 60 childbearing-age women. The samples were classified into three groups: healthy control (HC), bacterial vaginosis (BV), and BV intermediate (BVI). The number of Operational Taxonomic Units (OTUs) per sample ranged from 50 to 212, with three groups having 469 (HC), 482 (BVI), and 456 (BV) OTUs. Alpha diversity analysis (p < 0.05) showed that HC had lower diversity than the BV and BVI groups, whereas richness indices did not differ significantly across the groups. Beta diversity analysis (p < 0.05) indicated significant differences in species composition between groups, and specific biomarker taxa were identified for each group. Compared to HC, the BVI and BV groups showed an increase in Actinobacteria and Bacteroidetes, and a relative decrease in Bacillota. Overall, the vaginal microbiota of healthy women of childbearing age was in a state of absolute predominance of Lactobacillus, dominated by Lactobacillus crispatus or Lactobacillus iners alone, or both equally, and coexisted with a wide range of bacteria. However, patients in BVI group, Lactobacillus is reduced, dominated by L. iners, with an increased proportion of anaerobic bacteria (e.g., Gardnerella). While BV patients have predominantly Gardnerella with commensal bacteria, such as Prevotella and Fannyhessea, which collectively contribute to the development of BV. This study's findings provide insight into the dynamics of vaginal microbiota in women of childbearing age.

Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.

White gill disease (WGD) is one of the major diseases affecting Larimichthys crocea, although its etiology remains unclear. To investigate the causes of WGD, this study selected WGD-affected Larimichthys crocea (WG) and healthy Larimichthys crocea (NH) from multiple aquaculture regions for pathological analysis and analysis of bacterial and viral community characteristics. The results indicated severe tissue damage and significant inflammatory responses, as evidenced by clinical manifestations and electron microscopy. Two bacterial species, Photobacterium damselae and Vibrio campbellii, were isolated from all lesion tissues. Additionally, 16S full-length sequencing results showed that Photobacterium damselae and Vibrio campbellii dominated in the tissues of Larimichthys crocea, with a combined relative abundance of approximately 90 %. There were no significant differences in α-diversity and β-diversity between the NH group and WG group from the three aquaculture regions, and no significant biomarkers were identified. The diversity of DNA and RNA viruses did not show significant differences between the NH and WG groups, although both types of viruses exhibited notable synergistic and antagonistic relationships. Analyses from 16S full-length sequencing, metagenomics, and metatranscriptomics revealed that the related functional genes were primarily enriched in various metabolic pathways, including glycine biosynthesis, membrane transport, and energy metabolism. The metatranscriptomic analysis indicated that the expression levels of genes related to antibiotic resistance, biosynthesis, transport, and degradation processes were significantly downregulated in the WG group. Finally, through PCR, qPCR, and metagenomic sequencing, we were unable to detect iridovirus in Larimichthys crocea, further suggesting that the causes of WGD may differ across aquaculture regions compared to previous reports. This study indicates that the etiology of WGD may involve complex ecological and metabolic mechanisms, rather than being merely the result of a single pathogen infection. This research provides a comprehensive analysis of the microbial communities in WGD-affected Larimichthys crocea from multiple aquaculture regions for the first time, providing a theoretical basis for further elucidating the causes of WGD and developing preventive measures.

Baicalein has pharmacological functions, such as antioxidant and anti-inflammatory properties, and has been shown to alleviate damage to organs caused by environmental pollutants. However, the mechanism by which baicalein reduces the toxic effects of metals needs further research. This study used Pelophylax nigromaculatus tadpoles as a model to explore the toxicological effects of lead (Pb) on the gut-liver axis, and the mechanism by which baicalein alleviates lead toxicity. Analysis of the gut microbiota showed that baicalein alleviated abnormal changes in the gut microbiota following Pb exposure, mainly by increasing the abundance of beneficial bacterial genera, including Cetobacterium, Clostridioides, and Monoglobus. Liver metabolomics showed that compared to a natural recovery, baicalein treatment significantly increased the content of metabolites such as uridine, 17α-hydroxypregnenolone, niacin, and cucurbitacin E, and significantly reduced the content of metabolites such as linoleic, gluconic acid, and tetrahydrocortisone. These differential metabolites could be enriched in pathways such as pyrimidine metabolism, nicotinic acid and nicotinamide metabolism, and steroid hormone biosynthesis, which were beneficial for the treatment of liver injury. There was a significant correlation between the gut microbiota and the main differential metabolites in the liver with the addition of baicalein. The improvement of these metabolic pathways by baicalein is beneficial for the repair of the liver and intestines. Therefore, baicalein can increase the abundance of beneficial gut microbiota, improve liver metabolism, and thus reduce the damage of Pb exposure to the gut-liver axis.

Pacific Whiteleg shrimp (Litopenaeus vannamei) is an important model for breeding programs to improve global aquaculture productivity. However, the interaction between host genetics and microbiota in enhancing productivity remains poorly understood. We investigated the effect of two shrimp genetic lines, Fast-Growth (Gen1) and Disease-Resistant (Gen2), on the microbiota of L. vannamei.

Using genome-wide SNP microarray analysis, we confirmed that Gen1 and Gen2 represented distinct genetic populations. After confirming that the rearing pond did not significantly influence the microbiota composition, we determined that genetic differences explained 15.8% of the microbiota variability, with a stronger selective pressure in the hepatopancreas than in the intestine. Gen1, which exhibited better farm productivity, fostered a microbiota with greater richness, diversity, and resilience than Gen2, along with a higher abundance of beneficial microbes. Further, we demonstrated that a higher abundance of beneficial microbes was associated with healthier shrimp vs. diseased specimens, suggesting that Gen1 could improve shrimp's health and productivity by promoting beneficial microbes. Finally, we determined that the microbiota of both genetic lines was significantly different from their wild-type counterparts, suggesting farm environments and selective breeding programs strongly alter the natural microbiome.

This study highlights the importance of exploring the hologenome perspective, where integrating host genetics and microbiome composition can enhance breeding programs and farming practices.