Microbial Phenotypes Research Articles

Sputum metagenomics reveals a multidrug resistant Pseudomonas‐dominant severe asthma phenotype in an Asian population

AbstractBackground and ObjectiveWhile the lung microbiome in severe asthma has been studied, work has employed targeted amplicon‐based sequencing approaches without functional assessment with none focused on multi‐ethnic Asian populations. Here we investigate the clinical relevance of microbial phenotypes of severe asthma in Asians using metagenomics.MethodsProspective assessment of clinical, radiological, and immunological measures were performed in a multi‐ethnic Asian severe asthma cohort (N = 70) recruited across two centres in Singapore. Sputum was subjected to shotgun metagenomic sequencing and patients followed up for a 2‐year period. Metagenomic assessment of sputum microbiomes, resistomes and virulomes were related to clinical outcomes.ResultsThe lung microbiome in a multi‐ethnic Asian cohort with severe asthma demonstrates an increased abundance of Pseudomonas species. Unsupervised clustering of sputum metagenomes identified two patient clusters: C1 (n = 52) characterized by upper airway commensals and C2 (n = 18) dominated by established respiratory pathogens including M. catarrhalis, S. aureus and most significantly P. aeruginosa. C2 patients demonstrated a significantly increased exacerbation frequency on 2‐year follow up and an antimicrobial resistome characterized by multidrug resistance. Virulomes appear indistinguishable between severe asthmatics with or without co‐existing bronchiectasis, and C2 patients exhibit increased gene expression related to biofilm formation, effector delivery systems and microbial motility. Independent comparison of the C2 cluster to a non‐asthmatic bronchiectasis cohort demonstrates analogous airway microbial virulence patterns.ConclusionSputum metagenomics demonstrates a multidrug‐resistant Pseudomonas‐dominant severe asthma phenotype in Asians, characterized by poor clinical outcome including increased exacerbations which is independent of co‐existing bronchiectasis.

Dynamic changes in gut microbiota and production phenotypes driven by host genetic background in large yellow croaker

The gut microbiota is becoming increasingly important in enhancing aquaculture productivity. However, there are fewer studies on the effect of host genetic background on the gut microbiota of cultured fish. In the current study, we aimed to determine whether the genetic background of large yellow croaker influences differences in gut microbial composition and growth. To address this objective, we conducted a comparative experiment involving the nearshore cage culture of a selected line (SL) of large yellow croaker, which was subjected to genetic selection for swimming performance, alongside a control line (CL). Both lines were reared under identical environmental and dietary conditions for a duration of six weeks. We employed 16S rRNA gene sequencing technology to analyze the gut microbial composition of the large yellow croaker, and utilized bioinformatics methods to assess the abundance and diversity of the gut microbiota. The findings revealed that the core gut microbiota of both lines primarily comprised Proteobacteria, Firmicutes, and Bacteroidetes. However, a significant disparity in gut microbiota abundance was observed between SL and CL following nearshore cage culture. Additionally, the survival rate of SL reached 64.8 %, significantly higher than the 37.3 % observed in CL. The feed conversion efficiency of SL reached 47.7 %, significantly higher than that of CL (28.6 %). These results underscore the influence of host genetic background on driving differences in gut microbial community composition and production phenotypes. This research offers intriguing insights into the interconnectedness of gut microbiota, fish genetics, and production phenotypes.

Decoupled Nutrient Status: a framework to disentangle host from microbial responses to diets that vary in digestibility

Diet shapes the gut microbiome, which in turn influences host phenotype. Accordingly, there is much interest in leveraging diet to modulate gut microbial communities and host biology. However, recent approaches have not fully appreciated that hosts and gut microbes experience diet differently. Whether dietary nutrients reach the gut microbiota, which primarily resides in the colon in humans and other hindgut fermenters, depends on nutrient absorption in the small intestine. That gut microbes utilize the fraction of diet that escapes host-driven digestion creates a paradigm where host nutrient status is decoupled from, and often negatively correlated with, gut microbiota nutrient status. Here, we present a framework based on this concept of decoupled nutrient status (DNS), which can be used to understand distinct host and gut microbial phenotypes that are ultimately mediated by the small intestinal digestibility of the diet. We evaluate our framework against existing research employing diets of varying digestibility and demonstrate convergence of host phenotypes and gut microbial signatures across studies. Further, we highlight that gut microbial signatures predicted by DNS manifest most strongly in humans living industrialized lifestyles and in captive animals that habitually consume diets with high host-driven digestibility. We posit that the evolutionary decoupling of nutritional status between hosts and their gut microbiota has likely been especially pronounced in humans due to our intensified pursuit of calorie-rich, easy-to-digest diets. We conclude by proposing future research directions to better capture diet as it appears to gut microbes, a perspective likely to deliver new understanding of diet-microbiome interactions.

Hydrolyzed protein formula improves the nutritional tolerance by increasing intestinal development and altering cecal microbiota in low-birth-weight piglets.

Prematurity or low birth weight (LBW), poses a significant challenge in global health. Exploring appropriate and effective nutritional interventions is crucial for the growth and development of LBW infants. Hydrolyzed protein formula has been suggested as a potential solution to prevent intestinal dysfunction and improve digestion and absorption in infants. This study aimed to investigate the benefits of hydrolyzed protein formula on feeding intolerance, intestinal morphological development, and microbiota in a LBW piglet model. A total of 24 male piglets (3 d of age, 0.95-1.25 kg average BW) were assigned (8 pens/diet; 1 pigs/pen) into three dietary treatments and fed with a basic formula (BF), standard premature infant formula (SF) and hydrolyzed protein formula (HF) respectively, for 7 d. After the piglets sacrifice, growth performance, amino acid metabolism and intestinal morphology were assessed. 16S rRNA sequencing and microbial metabolic phenotypes analyzed the effects of different formula treatments on intestinal flora structure of LBW piglets. The HF diet reduced the rates of diarrhea and milk vomiting were reduced by 20.44% (p > 0.05) and 58.44% (p > 0.05), and decreased the crypt depth in the ileum while increasing the ratio of villus height/crypt depth and the mRNA expressions of y+LAT1 and b0,+AT in the ileum (p < 0.05). HF increased the final body weight, serum Thr and essential amino acid contents, and CAT2 and b0,+AT mRNA expressions in ileal mucosa compared with the SF diet (p < 0.05). Microbiota sequencing results showed that the colonic microbial richness indices (Chao1, ACE, and observed species), the diversity indices (Shannon and Simpson), and the phyla Actinobacteriota, unidentified_Bacteria, Acidobacteriota and Actinobacteria, the genus Rubrobacter and RB41 were reduced (p < 0.05) in SF and HF groups. Microbial metabolic phenotypes analysis showed a reduction in the richness of biofilm-forming bacteria (p < 0.05). In summary, hydrolyzed protein formula had better nutrition and tolerance in LBW suckling piglets by improving amino acid transport and intestinal development, and regulating gut microbial communities.

Enrichment Characteristics and Ecological Risk Prediction of Pathogens on Typical Microplastic Biofilms

As an emerging niche colonized by microorganisms, microplastics may selectively enrich pathogens, resulting in crucial ecological risks and potential threats to public health in aquatic environments. However, the enrichment characteristics and ecological risks of pathogens on different microplastic biofilms remain unclear. In this study, 16S rRNA high-throughput sequencing technology was used to investigate the differences in the bacterial community structure, occurrence characteristics of pathogens, and prediction of ecological risks on five typical microplastic biofilms of polyethylene （PE）, polypropylene （PP）, polystyrene （PS）, polyethylene terephthalate （PET）, and polyvinyl chloride （PVC） through a field in-situ incubation experiment. The results showed that after 28 d of in situ incubation, the macroscopic biofilms were formed on the surface of all microplastics, and the diversity and richness of the bacterial community on all microplastic biofilms were higher than in the surrounding water, indicating that the microorganisms in the surrounding water were selectively enriched on microplastics. Each type of microplastic biofilm had formed a unique bacterial community structure； in particular, PVC microplastics were more inclined to selectively enrich the members of Proteobacteria. A total of 47 human pathogens were identified using the HPB database, including six antibiotic resistance pathogens belonging to the lists of critical priority control. The number and total abundance of human pathogens detected on microplastic biofilm were higher than those in the surrounding water, and the dominant pathogens such as Bartonella, Burkholderia, and Brucella were selectively enriched on microplastic biofilms. Microbial phenotype prediction results based on BugBase showed that three functional phenotypes including biofilm formation, mobile element contained, and potentially pathogenic on microplastic biofilms had significantly increased by 2.38%-5.57%, 0.82%-7.13%, and 3.04%-8.30%, respectively, which were mainly contributed by α-Proteobacteria and γ-Proteobacteria. These results not only indicate that the selective enrichment of opportunistic pathogens on microplastic biofilms may lead to the increased risk of pathogenicity and antibiotic resistance co-spread but also provide reference for the accurate assessment of ecological risks caused by microplastic pollution in aquatic environments.

Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes.

Plants serve as critical links between above- and below-ground microbial communitites, both influencing and being influenced by microbes in these two realms. Below-ground microbial communities are expected to respond to soil resource environments, which are mediated by the roots of plants that can, in turn, be influenced by the above-ground community of foliar endophytes. For instance, diverse plant communities deposit more, and more diverse, nutrients into the soil, and this deposition is often increased when foliar pathogens are removed. Differences in soil resources can alter soil microbial composition and phenotypes, including inhibitory capacity, resource use, and antibiotic resistance. In this work, we consider plots differing in plant richness and application of foliar fungicide, evaluating consequences on soil resource levels and root-associated Streptomyces phenotypes. Soil carbon, nitrogen, phosphorus, potassium, and organic matter were greater in samples from polyculture than monoculture, yet this increase was surprisingly offset when foliar fungal communities were disrupted. We find that Streptomyces phenotypes varied more between richness plots-with the Streptomyces from polyculture showing lower inhibitory capacity, altered resource-use profiles, and greater antibiotic resistance-than between subplots with/without foliar fungicide. Where foliar fungicide affected phenotypes, it did so differently in polyculture than in monoculture, for instance decreasing niche width and overlap in monoculture while increasing them in polyculture. No differences in phenotype were correlated with soil nutrient levels, suggesting the need for further research looking more closely at soil resource diversity and particular compounds that were found to differ between treatments.

Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.

To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.

Microbial degradation of contaminants of emerging concern: metabolic, genetic and omics insights for enhanced bioremediation.

The perpetual release of natural/synthetic pollutants into the environment poses major risks to ecological balance and human health. Amongst these, contaminants of emerging concern (CECs) are characterized by their recent introduction/detection in various niches, thereby causing significant hazards and necessitating their removal. Pharmaceuticals, plasticizers, cyanotoxins and emerging pesticides are major groups of CECs that are highly toxic and found to occur in various compartments of the biosphere. The sources of these compounds can be multipartite including industrial discharge, improper disposal, excretion of unmetabolized residues, eutrophication etc., while their fate and persistence are determined by factors such as physico-chemical properties, environmental conditions, biodegradability and hydrological factors. The resultant exposure of these compounds to microbiota has imposed a selection pressure and resulted in evolution of metabolic pathways for their biotransformation and/or utilization as sole source of carbon and energy. Such microbial degradation phenotype can be exploited to clean-up CECs from the environment, offering a cost-effective and eco-friendly alternative to abiotic methods of removal, thereby mitigating their toxicity. However, efficient bioprocess development for bioremediation strategies requires extensive understanding of individual components such as pathway gene clusters, proteins/enzymes, metabolites and associated regulatory mechanisms. "Omics" and "Meta-omics" techniques aid in providing crucial insights into the complex interactions and functions of these components as well as microbial community, enabling more effective and targeted bioremediation. Aside from natural isolates, metabolic engineering approaches employ the application of genetic engineering to enhance metabolic diversity and degradation rates. The integration of omics data will further aid in developing systemic-level bioremediation and metabolic engineering strategies, thereby optimising the clean-up process. This review describes bacterial catabolic pathways, genetics, and application of omics and metabolic engineering for bioremediation of four major groups of CECs: pharmaceuticals, plasticizers, cyanotoxins, and emerging pesticides.

Aluminum-induced oxidative stress promotes changes in the structure of the gut microbiota and liver deficiency

As a low-toxicity metal, aluminum has garnered increasing attention in relation to its impact on the human body; however, the specific mechanism of action remains unclear. To bridge this knowledge gap and facilitate practical applications, this study took 8-week-old ICR mice as the research object to study the effects of dietary addition of aluminum potassium sulfate on intestinal flora structure and liver. As the concentration of aluminum increased, it inhibited mice weight growth rate and significantly altered the composition of white blood cells in their bloodstream. Histological examination revealed liver inflammation through HE staining sections. The oxidative stress markers MDA increased, GSH-PX and CAT decreased significantly. And liver function index MAO increased, TC and ALP decreased first and then increased. Moreover, there was a significant increase in pro-inflammatory factor TNF-α content. Further 16S rRNA sequencing analysis demonstrated substantial changes in both composition and structure of mouse intestinal microbiota induced by aluminum exposure; microbial phenotype prediction indicated that aluminum-induced oxidative stress promoted an increase in abundance of oxidation-resistant microbial types. Alterations in gut flora structure also influenced the liver via the gut-liver axis. These findings lay a foundation for further research on the regulation and interaction of aluminum on intestinal flora.

Heterogenetic mechanism in multidimensional pit mud with different fermentation years: From microbial structure dynamic succession to metabolism phenotypes

Pit mud (PM) is fermenting agents in the strong-flavor baijiu (SFB) production. In this paper, the discrepancies in fermentation parameters, microbial community succession patterns and metabolic phenotypes were compared in multidimensional PMs. The results showed that pyruvic acid, succinic acid, S-Acetyldihydrolipoamide-E, glycerol and glyceric acid were the key metabolites responsible for the metabolic differences between the 2-, 30-,100- and 300-year multidimensional PMs, while the butanoic acid, heptyl, heptanoic acid, heptanoic acid ethyl ester, hexanoic acid and octanoic acid were the key differential flavor compounds in the 2-, 30-,100- and 300-year multidimensional PMs. Concurrently, the diversity and abundance of microbial community also exhibited significant differences between the new and old multidimensional PMs, the assembly pattern of bacterial communities changed from deterministic to stochasticity from lower (bottom of the pit and under the huangshui fluid) to upper PM (up the huangshui fluid and top of the pit). Key microorganisms related to the succession process of the lower PM were Clostridium, Methanobacterium, Petrimonas, Lactobacillus, Methanobrevibacter, Bellilinea, Longilinea, Bacillus. In contrast, the upper PM were Caproicibacter, Longilinea, Lactobacillus, Proteinphilum, Methanobrevibacter, Methanobacterium, Methanobacteriaceae, Petrimonas, Bellilinea and Atopobium. Redundancy analysis (RDA) indicated that the key environmental factors regulating the succession of microbial in upper PM were lactic acid, moisture, pH and available phosphorus. In contrast, the lower was lactic acid, acetic acid and ammonia N. Based on these results, heterogeneous mechanisms between new and old multidimensional PMs were explored, providing a theoretical support for improving the quality of new PM.

Impact of Fecal Microbial Transplant Donor Inflammatory Phenotype on Tissue Inflammation in Humanized Mouse Models After a High-Fat Diet

Impact of Fecal Microbial Transplant Donor Inflammatory Phenotype on Tissue Inflammation in Humanized Mouse Models After a High-Fat Diet

Relationship between Rumen Microbial Differences and Phenotype Traits among Hu Sheep and Crossbred Offspring Sheep.

This experiment was conducted to investigate the effect of three-way hybrid sheep and Hu sheep on serum indicators, rumen fermentation, rumen enzyme activity, and microorganisms in sheep. Healthy and similar birth weights from three groups (Hu, n = 11; Charolais × Australian White × Hu, CAH, n = 11; Charolais × Dorper × Hu, CDH, n = 11) were selected to be fed by the ewes until 45 days of age. Subsequently, they were weaned intensively and underwent short-term fattening for 3 months along with selected male lambs fed intensively. During this period, they were fed and watered ad libitum. Blood and rumen fluid were collected and analyzed for serum indicators and rumen fluid microorganisms, enzyme activity, and VFA, respectively, at the end of the fattening period. Compared with Hu lamb, the offspring of the three-way hybrid lamb showed significant improvements in body weight, serum lactate dehydrogenase, and creatinine content. However, there was no significant effect on serum immunity and antioxidant indices. In addition, the rumen fluid volatile fatty acid (VFA) molar concentration and microcrystalline cellulose and lipase content were significantly lower in the three-way hybrid lamb compared to Hu lamb, but β-glucosidase, amylase, pepsin, and VFA molar ratio were not significantly affected. Subsequently, 16S rRNA sequencing diversity analysis revealed that three-way hybrid lamb significantly increased rumen microbial ACE and Chao1 indices compared to Hu lamb. Meanwhile, the abundance of Verrucomicrobiota and Synergistota significantly increased at the phylum level. Correlation analysis showed that Prevotella had the highest proportion, while Rikenellaceae_RC9_gut_group correlated most closely with others genus. The microbial communities isovaleric acid molar concentration and proportion were strongly correlated. In addition, there were significant differences in correlations between microbial communities and isobutyric acid, butyric acid and valeric acid content, and their molar proportion, but they were not significantly correlated with digestive enzymes. From the functional enrichment analysis, it was found that hybrid progeny were mainly enriched in the pyruvate metabolism, microbial metabolism in diverse environments, carbon metabolism, and quorum sensing pathways. In contrast, the Hu sheep were primarily enriched in the cysteine and methionine, amino sugar and nucleotide sugar, and biosynthesis of secondary metabolite pathways. These results suggest that hybridization can play a role in regulating organismal metabolism and improve animal production performance by influencing the structure and characteristics of microbial communities.

Microbial Diversity and Community Structure of Chinese Fresh Beef during Cold Storage and Their Correlations with Off-Flavors.

To investigate the diversity and dynamics of microorganisms in Chinese fresh beef (CFB) without acid discharge treatment during cold storage, high-throughput sequencing was employed to analyze the CFB refrigerated for 0, 3, 7, and 10 days. The results showed that the community richness of the fungi and bacteria decreased significantly. However, the diversity decreased in the early stage and increased in the later stage. At the phylum level, Ascomycota (74.1-94.1%) and Firmicutes (77.3-96.8%) were the absolutely dominant fungal and bacterial phyla. The relative abundance of both fungal and bacterial phyla displayed a trend of increasing and then decreasing. At the genus level, Candida (29.3-52.5%) and Lactococcus (19.8-59.3%) were, respectively, the dominant fungal and bacterial genera. The relative abundance of Candida showed a trend of increasing and then decreasing, while Lactococcus possessed the opposite trend. KEGG metabolic pathways analysis suggested that carbohydrate metabolism, membrane transport, and amino acid metabolism were the major metabolic pathways of bacteria. Bugbase prediction indicated the major microbial phenotype of bacteria in CFB during cold storage was Gram-positive (17.2-31.6%). Correlation analysis suggested that Lactococcus, Citrobacter, Proteus, and Rhodotorula might be the main microorganisms promoting the production of off-flavor substances in CFB. This study provides a theoretical basis for the preservation of Chinese fresh beef.

Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions.

Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.

Distinct compositions and functions of circulating microbial DNA in the peripheral blood compared to fecal microbial DNA in healthy individuals.

The crucial function of circulating microbial DNA (cmDNA) in peripheral blood is gaining recognition because of its importance in normal physiology and immunity in healthy individuals. Evidence suggests that cmDNA in peripheral blood is derived from highly abundant, translocating gut microbes. However, the associations with and differences between cmDNA in peripheral blood and the gut microbiome remain unclear. We collected blood, urine, and fecal samples from volunteers to compare their microbial information via 16S rDNA sequencing. The results revealed that, compared with gut microbial DNA, cmDNA in peripheral blood was associated with reduced diversity and a distinct microbiota composition. The cmDNA in the blood reflects the biochemical processes of microorganisms, including synthesis, energy conversion, degradation, and adaptability, surpassing that of fecal samples. Interestingly, cmDNA in blood showed a limited presence of DNA from anaerobes and gram-positive bacteria, which contrast with the trend observed in fecal samples. Furthermore, analysis of cmDNA revealed traits associated with mobile elements and potential pathologies, among others, which were minimal in stool samples. Notably, cmDNA analysis indicated similarities between the microbial functions and phenotypes in blood and urine samples, although greater diversity was observed in urine samples. Source Tracker analysis suggests that gut microbes might not be the main source of blood cmDNA, or a selective mechanism allows only certain microbial DNA into the bloodstream. In conclusion, our study highlights the composition and potential functions associated with cmDNA in peripheral blood, emphasizing its selective presence; however, further research is required to elucidate the mechanisms involved.IMPORTANCEOur research provides novel insights into the unique characteristics and potential functional implications of circulating microbial DNA (cmDNA) in peripheral blood. Unlike other studies that analyzed sequencing data from fecal or blood microbiota in different study cohorts, our comparative analysis of cmDNA from blood, urine, and fecal samples from the same group of volunteers revealed a distinct blood-specific cmDNA composition. We discovered a decreased diversity of microbial DNA in blood samples compared to fecal samples as well as an increased presence of biochemical processes microbial DNA in blood. Notably, we add to the existing knowledge by documenting a reduced abundance of anaerobes and gram-positive bacteria in blood compared to fecal samples according to the analysis of cmDNA and gut microbial DNA, respectively. This observation suggested that a potential selective barrier or screening mechanism might filter microbial DNA molecules, indicating potential selectivity in the translocation process which contrasts with the traditional view that cmDNA primarily originates from random translocation from the gut and other regions. By highlighting these differences, our findings prompt a reconsideration of the origin and role of cmDNA in blood circulation and suggest that selective processes involving more complex biological mechanisms may be involved.

Effects of cutting height and storage length on fermentation characteristics, microbial community, co-occurrence networks, potential functionality and pathogenic risk of fermented sweet sorghum stem

Postharvest management strategies like cutting height and anaerobic fermentation may affect the microbial risk of vegetables. This study evaluated the effects of cutting height and storage length on the fermentation characteristics, microbial diversity, co-occurrence networks, potential functionality and pathogenic risk of sweet sorghum stem (SSS). Fresh SSS harvested at two cutting heights (15 cm, F15; 45 cm, F45) was spontaneously fermented (S15 and S45) for 2, 4, 8, 16, 32 and 64 days. Decreasing the cutting height of SSS increased the dry matter, water-soluble carbohydrate content as well as Acinetobacter (23.0% vs. 44.9%) and Klebsiella (1.84% vs. 6.58%) proportion but decreased the crude protein content (P < 0.05). After fermentation, both cutting heights presented desirable fermentation. Anaerobic fermentation promoted the Glycolysis pathway (0.009 vs. 0.018) and related enzymes (l-lactate dehydrogenase, etc.) associated with lactate synthesis, but suppressed the degradation pathways of valine, leucine, isoleucine (0.011 vs. 0.003) and lysine (0.008 vs. 0.002). In microbial phenotype analysis, although F15 had higher proportions of ‘Potentially Pathogenic’ than F45, this undesirable phenotype declined to negligible levels via fermentation. These results concluded that, for SSS, concerns about the risk of microbial contamination and pathogens from low cutting height can be dispelled by well fermentation.

Effects of Aquaculture and Thalassia testudinum on Sediment Organic Carbon in Xincun Bay, Hainan Island

Eutrophication due to aquaculture can cause the decline of seagrasses and impact their carbon storage capacity. This study explored the effects of aquaculture on the sediment organic carbon (SOC) in Thalassia testudinum seagrass beds using enzyme activity and microorganisms as indicators. Our results showed that the distance to aquaculture significantly increased the SOC and TN of sediments; the C/N ratio of sediments was reduced by the distance to aquaculture. Distance to aquaculture and seagrasses significantly impacted the δ13C of sediments, and their significant interactive effects on the δ13C of sediments were found. Distance to aquaculture and seagrasses had significantly interactive effects on the cellulase activity of sediments. Distance to aquaculture and seagrasses separately reduced the invertase activity of sediments. SOC in the seagrass bed was significantly positively impacted by cellulase activity and polyphenol oxidase activity in sediments. Firmicutes, Desulfobacterota and Chloroflexi were the dominant taxa in the S1 and S2 locations. From the S1 location to the S2 location, the relative abundances of Firmicutes and Desulfobacterota increased. The functional profiles of COG were relatively similar between the S1 and S2 locations. BugBase phenotype predictions indicated that the microbial phenotypes of all the seagrass sediment samples were dominated by anaerobic bacteria in terms of oxygen utilizing phenotypes. FAPROTAX functional predictions indicated that aquaculture affects functions associated with seagrass bed sediment bacteria, particularly those related to carbon and nitrogen cycling. This study can provide an important basis for understanding the response mechanism of global carbon sink changes to human activities such as aquaculture and supply more scientific data for promoting the conservation and management of seagrass beds.

Effects of Hawthorn Flavonoids on Intestinal Microbial Community and Metabolic Phenotype in Obese Rats.

Obesity (OB) is a prevalent metabolic disorder. With the advancement of the economy, the prevention and treatment of obesity is a big problem for the global community. The methods to lose weight include exercise, diet, medicine, and surgery. Compared with other methods, diet regulation is safer and more effective. Hawthorn fruit has the effect of reducing weight, but the mechanism of effectiveness are not clear. In this study, obesity model rats are used to conduct scientific pharmacological research on hawthorn flavonoids. Hawthorn flavonoids can effectively improve the body weight, lipid accumulation, and lipid levels of obese rats. The contents of the colon of rats are analyzed using 16S rDNA sequencing technology. The intestinal microflora in obese rats changed significantly after flavonoids treatment, and they tended to be the control group. Based on liquid chromatography-mass spectrometry, serum metabolomics showed that the metabolites in the serum changed significantly, after hawthorn flavonoids treatment. Hawthorn flavonoids are especially involved in the biological processes of grade bile acid biosynthesis, histidine metabolism, and lipid metabolism. Pearson correlation analysis showed that the disorder of intestinal microorganisms is connected to changes in serum metabolites. These findings give a new idea about how hawthorn flavonoids help with obesity.

Effects of selenium-enriched yeast dietary supplementation on egg quality, gut morphology and caecal microflora of laying hens

Selenium (Se) is an essential micronutrient for humans and animals and is a powerful antioxidant that can promote reproductive and immune functions. The purpose of this study was to evaluate the effects of supplemental dietary selenium-enriched yeast (SeY) on egg quality, gut morphology and microflora in laying hens. In total, 100 HY-Line Brown laying hens (45-week old) were randomly allocated to two groups with 10 replicates and fed either a basal diet (without Se supplementation) or a basal diet containing 0.2 mg/kg Se in the form of SeY for 8 weeks. The Se supplementation did not have a significant effect on egg quality and intestinal morphology of laying hens. Based on the 16S rRNA sequencing, SeY dietary supplementation effectively modulated the cecal microbiota structure. An alpha diversity analysis demonstrated that birds fed 100 mg/kg SeY had a higher cecal bacterial diversity. SeY dietary addition elevated Erysipelotrichia (class), Lachnospiraceae (family), Erysipelotrichaceae (family) and Ruminococcus_torques_group (genus; p < .05). Analysis of microbial community-level phenotypes revealed that SeY supplementation decreased the microorganism abundance of facultatively anaerobic and potentially pathogenic phenotypes. Overall, SeY supplementation cannot significantly improve intestinal morphology; however, it modulated the composition of cecal microbiota toward a healthier gut.

Uncovering the impact of sea mud-containing diet on fecal fragmentation and its potential environmental risks in recirculating aquaculture system of Apostichopus japonicus

A deep understanding of fecal characteristics and fragmentation mechanism is crucial for effectively removing the solid particles in recirculating aquaculture system (RAS) of Apostichopus japonicus, however, the underlying mechanism was still unclear. This study investigated the effects of diet with different sea mud addition on the fecal characteristics and microbiota. The experimental diet were the mixture of commercial feed and sea mud at the ratio of 1:1, 1:2, 1:3, 1:4 and 1:5, in which the added amount of sea mud was 50 %, 66.67 %, 75 %, 80 % and 83.33 %, respectively. The results showed that, at the end of aquaculture, Dx(50) in group 1:3 was the highest, while group 1:5 was the lowest. The fecal particle size distribution (PSD) appeared multi peak with the increase of sea mud addition. At the end of aquaculture, group 1:3 possessed the highest microbial diversity. BugBase phenotype prediction found that the microbial phenotypes in group 1:4 were mainly involved in functional expression, such as stress tolerance and potential pathogenicity. Significant correlation between environmental factors and fecal microbiota were found. Correlation analysis between fecal particle size and fecal microbiota showed that the abundance of pathogenic bacteria such as Vibrio, was higher on fecal particles with dispersed PSD. And NH4+-N removal rate decreased when Dx(10) decreased and Dx(90) increased. Thus, it was recommended that sea mud addition in diet should be <75 % in A. japonicus RAS.