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Microbiome Oct 2023Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported...
BACKGROUND
Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported that the gut bacterial community induced by BFS is highly associated with shrimp disease resistance, the causal relationship remains unknown. Here, the promotive roles of gut bacterial community induced by BFS in pathogenic Vibrio infection resistance and its potential micro-ecological and physiological mechanisms were investigated by gut bacterial consortium transplantation and synthetic community (SynCom) construction.
RESULTS
The BFS induced a more stable and resistant gut bacterial community, and significantly enriched some beneficial bacterial taxa, such as Paracoccus, Ruegeria, Microbacterium, Demequina, and Tenacibaculum. Transplantation of a gut bacterial consortium from BFS shrimp (Enrich) greatly enhanced the stability of the bacterial community and resistance against pathogenic V. parahaemolyticus infection in WES shrimp, while transplantation of a gut bacterial consortium from WES shrimp significantly disrupted the bacterial community and increased pathogen susceptibility in both WES and BFS shrimp. The addition of Enrich in shrimp postlarvae also improved the pathogen resistance through increasing the relative abundances of beneficial bacterial taxa and stability of bacterial community. The corresponding strains of five beneficial bacterial taxa enriched in BFS shrimp were isolated to construct a SynCom. The addition of SynCom could not only suppress disease development, but also improve shrimp growth, boost the digestive and immune activities, and restore health in diseased shrimp. Furthermore, the strains of SynCom well colonized shrimp gut to maintain a high stability of bacterial community.
CONCLUSIONS
Our study reveals an important role for native microbiota in protecting shrimp from bacterial pathogens and provides a micro-ecological regulation strategy towards the development of probiotics to ameliorate aquatic animal diseases. Video Abstract.
Topics: Animals; Vibrio parahaemolyticus; Gastrointestinal Microbiome; Penaeidae; Bacteria; Vibrio Infections; Aquaculture
PubMed: 37858205
DOI: 10.1186/s40168-023-01663-2 -
Microorganisms Sep 2023Pachymaran (PCP), the major medicinal constituent of Poria cocos, has a regulatory effect on immunosuppressive lung injury, but its mechanism of action with respect to...
Pachymaran (PCP), the major medicinal constituent of Poria cocos, has a regulatory effect on immunosuppressive lung injury, but its mechanism of action with respect to gut microorganisms and their metabolites is not clear. The aim of this study was to investigate the protective effect of PCP against immunosuppressive lung injury caused by cyclosporine A (CsA), and to reveal its possible mechanism of action via the comprehensive analysis of 16S rRNA and LC-MS. We demonstrated that PCP was effective at alleviating CsA-induced immunosuppressive lung injury by restoring the organ indices and lung tissue morphology and structure. PCP significantly altered the composition of the gut and lung microbiota in mice with CsA-induced immunosuppressive lung injury by increasing the number of beneficial bacteria from the , , , and , and reducing the pathogenic to fulfill its immunomodulatory role. In lung tissue microecology, PCP intervention significantly reduced the abundance of , , , and and increased the abundance of . The LC-MS results showed that PCP alleviated the CsA-induced immunosuppression of lung tissue injury. The model serum metabolite Americine decreased the expression of PC(O-18:1(4Z)/0:0). Our results suggest that PCP may be involved in regulating the composition, function, and metabolism of the gut and lung microbiota to reverse CsA-induced immunosuppressive lung injury.
PubMed: 37764093
DOI: 10.3390/microorganisms11092249 -
Microbiology Spectrum Sep 2023Sulfamethoxazole (SMX), as one of the most widely used sulfonamide antibiotics, has been frequently detected in the aqueous environment, posing potential risks to the...
Sulfamethoxazole (SMX), as one of the most widely used sulfonamide antibiotics, has been frequently detected in the aqueous environment, posing potential risks to the environment and human health. Although microbial degradation methods have been widely applied, some issues remain, including low degradation efficiency and poor environmental adaptability. In this regard, constructing efficient degrading bacteria by metabolic engineering is an ideal solution to these challenges. In this study, we used DYTN-1, a superior nitrogen removal environment strain, as chassis to construct an SMX degradation pathway, obtaining a new bacteria for simultaneous degradation of SMX and removal of ammonia nitrogen. In doing this, we first identified and characterized four native promoters of DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. After degradation pathway expression level optimization and FMN reductase optimization, SMX degradation efficiency was significantly improved. The constructed pIAB-P strain exhibited superior co-degradation of SMX and ammonia nitrogen contaminants with degradation rates of 44% and 71%, respectively. This study could pave the way for SMX degradation engineered strain design and evolution of environmental bioremediation. IMPORTANCE The abuse of sulfamethoxazole (SMX) had led to an increased accumulation in the environment, resulting in the disruption of the structure of microbial communities, further disrupting the bio-degradation process of other pollutants, such as ammonia nitrogen. To solve this challenge, we first identified and characterized four native promoters of DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. Then SMX degradation efficiency was significantly improved with degradation pathway expression level optimization and FMN reductase optimization. Finally, the superior nitrogen removal environment strain, DYTN-1, obtained an SMX degradation function. This pioneering study of metabolic engineering to enhance the SMX degradation in microorganisms could pave the way for designing the engineered strains of SMX and nitrogen co-degradation and the environmental bioremediation.
PubMed: 37732744
DOI: 10.1128/spectrum.00146-23 -
Scientific Reports Sep 2023Gut microbiota is an emerging editable cardiovascular risk factor. We aim to investigate gut and coronary plaque microbiota, using fecal samples and angioplasty balloons...
Gut microbiota is an emerging editable cardiovascular risk factor. We aim to investigate gut and coronary plaque microbiota, using fecal samples and angioplasty balloons from patients with acute coronary syndrome (ACS), chronic coronary syndrome (CCS) and control subjects. We examined bacterial communities in gut and coronary plaques by 16S rRNA sequencing and we performed droplet digital PCR analysis to investigate the gut relative abundance of the bacterial genes CutC/CntA involved in trimethylamine N-oxide synthesis. Linear discriminant analysis effect size (LEfSe) at the genus and species levels displayed gut enrichment in Streptococcus, Granulicatella and P. distasonis in ACS compared with CCS and controls; Roseburia, C. aerofaciens and F. prausnitzii were more abundant in controls than in patients. Principal component analysis (PCA) of 41 differentially abundant gut taxa showed a clustering of the three groups. In coronary plaque, LEfSe at the genus level revealed an enrichment of Staphylococcus and Streptococcus in ACS, and Paracoccus in CCS, whereas PCA of 15 differentially abundant plaque taxa exhibited clustering of ACS and CCS patients. CutC and CntA genes were more abundant in ACS and CCS than in controls while no significant difference emerged between ACS and CCS. Our results indicate that ACS and CCS exhibit a different gut and plaque microbial signature, suggesting a possible role of these microbiotas in coronary plaque instability.
Topics: Humans; Acute Coronary Syndrome; RNA, Ribosomal, 16S; Heart; Angioplasty, Balloon; Carnobacteriaceae
PubMed: 37679428
DOI: 10.1038/s41598-023-41867-y -
Toxics Aug 2023Nitrification inhibitors are recognized as a key approach that decreases the denitrification process to inhibit the loss of nitrogen to the atmosphere in the form of NO....
Nitrification inhibitors are recognized as a key approach that decreases the denitrification process to inhibit the loss of nitrogen to the atmosphere in the form of NO. Targeting denitrification microbes directly could be one of the mitigation approaches. However, minimal attempts have been devoted towards the development of denitrification inhibitors. In this study, we aimed to investigate the molecular docking behavior of the nitrous oxide reductase (NOR) and nitrite reductase (NIR) involved in the microbial denitrification pathway. Specifically, in silico screening was performed to detect the inhibitors of nitrous oxide reductase (NOR) and nitrite reductase (NIR) using the PatchDock tool. Additionally, a toxicity analysis based on insecticide-likeness, Bee-Tox screening, and a STITCH analysis were performed using the SwissADME, Bee-Tox, and pkCSM free online servers, respectively. Among the twenty-two compounds tested, nine ligands were predicted to comply well with the TICE rule. Furthermore, the Bee-Tox screening revealed that none of the selected 22 ligands exhibited toxicity on honey bees. The STITCH analysis showed that two ligands, namely procyanidin B2 and thiocyanate, have interactions with both the and microbial proteins. The molecular docking results indicated that ammonia exhibited the second least atomic contact energy (ACE) of -15.83 kcal/mol with nitrous oxide reductase (NOR) and an ACE of -15.20 kcal/mol with nitrite reductase (NIR). The inhibition of both the target enzymes (NOR and NIR) supports the view of a low denitrification property and suggests the potential future applications of natural/synthetic compounds as significant nitrification inhibitors.
PubMed: 37624165
DOI: 10.3390/toxics11080660 -
Environment International Aug 2023The polyethylene (PE) film mulching as a water conservation technology has been widely used in dryland agriculture, yet the long-term mulching has led to increasing...
The polyethylene (PE) film mulching as a water conservation technology has been widely used in dryland agriculture, yet the long-term mulching has led to increasing accumulation of secondary pollutants in soils. The decomposition of PE film-sourced pollutants is directly associated with the enrichment of specific bacterial communities. We therefore hypothesized that plant biomass may act as an organic media to mediate the pollutant decomposition via reshaping bacterial communities. To validate this hypothesis, plant biomass (dried maize straw and living clover) was embedded at the underlying surface of PE film, to track the changes in the composition and function of bacterial communities in maize field across two years. The results indicated that both dry crop straw and alive clover massively promoted the α-diversity and abundance of dominant bacteria at plastisphere, relative to bulk soil. Bacterial communities tended to be clustered at plastisphere, forming the bacteria islands to enrich pollutant-degrading bacteria, such as Sphingobacterium, Arthrobacter and Paracoccus. As such, plastisphere bacteria islands substantially enhanced the degradation potential of chloroalkene and benzoate (p < 0.05). Simultaneously, bacterial network became stabilized and congregated at plastisphere, and markedly improved the abundance of plastisphere module hubs and connectors bacteria via stochastic process. Particularly, bacterial community composition and plastic film-sourced pollutants metabolism were evidently affected by soil pH, carbon and nitrogen sources that were mainly derived from the embedded biomass. To sum up, plant biomass embedding as a nature-based strategy (NbS) can positively mediate the decomposition of plastic-sourced pollutants through plastisphere bacteria island effects.
Topics: Soil; Biomass; Polyethylene; Environmental Pollutants; Water; Agriculture; Plastics; Bacteria; Soil Microbiology
PubMed: 37499460
DOI: 10.1016/j.envint.2023.108114 -
International Journal of Molecular... Jun 2023The circulation is a closed system that has been assumed to be free from bacteria, but evidence for the existence of a low-density blood microbiota is accumulating. The...
The circulation is a closed system that has been assumed to be free from bacteria, but evidence for the existence of a low-density blood microbiota is accumulating. The present study aimed to map the blood microbiota of outpatients with Crohn's disease (CD) or with ulcerative colitis (UC) by 16S metagenomics. A diverse microbiota was observed in the blood samples. Regardless of the type of disease, the alpha diversity of the microbiota was positively associated with C-reactive protein (CRP). The blood microbiota had a surprisingly high proportion of in comparison with human oral and colonic microbiotas. There was no clear difference in the overall pattern of the microbiota between CD and UC. A non-template control (NTC) was included in the whole process to control for the potential contamination from the environment and reagents. Certain bacterial taxa were concomitantly detected in both blood samples and NTC. However, , , and were found in blood from both CD and UC patients but not in NTC, indicating the existence of a specific blood-borne microbiota in the patients. dominated in all blood samples, but a minor amount was also found in NTC. was significantly enriched in CD, but it was also detected in high abundance in NTC. Whether the composition of the blood microbiota could be a marker of a particular phenotype in inflammatory bowel disease (IBD) or whether the blood microbiota could be used for diagnostic or therapeutic purposes deserves further attention.
Topics: Humans; C-Reactive Protein; Outpatients; Inflammatory Bowel Diseases; Colitis, Ulcerative; Crohn Disease; Microbiota
PubMed: 37446076
DOI: 10.3390/ijms241310899 -
Frontiers in Endocrinology 2023The female reproductive tract harbours unique microbial communities (known as microbiota) which have been associated with reproductive functions in health and disease....
INTRODUCTION
The female reproductive tract harbours unique microbial communities (known as microbiota) which have been associated with reproductive functions in health and disease. While endometrial microbiome studies have shown that the uterus possesses higher bacterial diversity and richness compared to the vagina, the knowledge regarding the composition of the Fallopian tubes (FT) is lacking, especially in fertile women without any underlying conditions.
METHODS
To address this gap, our study included 19 patients who underwent abdominal hysterectomy for benign uterine pathology, and 5 women who underwent tubal ligation as a permanent contraceptive method at Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA). We analyzed the microbiome of samples collected from the FT and endometrium using 16S rRNA gene sequencing.
RESULTS
Our findings revealed distinct microbiome profiles in the endometrial and FT samples, indicating that the upper reproductive tract harbors an endogenous microbiome. However, these two sites also shared some similarities, with 69% of the detected taxa Being common to both. Interestingly, we identified seventeen bacterial taxa exclusively present in the FT samples, including the genera , and , among others. On the other hand, 10 bacterial taxa were only found in the endometrium, including the genera and (FDR <0.05). Furthermore, our study highlighted the influence of the endometrial collection method on the findings. Samples obtained transcervically showed a dominance of the genus Lactobacillus, which may indicate potential vaginal contamination. In contrast, uterine samples obtained through hysterescopy revealed higher abundance of the genera , and .
DISCUSSION
Although the upper reproductive tract appears to have a low microbial biomass, our results suggest that the endometrial and FT microbiome is unique to each individual. In fact, samples obtained from the same individual showed more microbial similarity between the endometrium and FT compared to samples from different women. Understanding the composition of the female upper reproductive microbiome provides valuable insights into the natural microenvironment where processes such as oocyte fertilization, embryo development and implantation occur. This knowledge can improve fertilization and embryo culture conditions for the treatment of infertility.
Topics: Female; Humans; RNA, Ribosomal, 16S; Uterus; Endometrium; Vagina; Infertility; Bacteria
PubMed: 37415669
DOI: 10.3389/fendo.2023.1096050 -
Microorganisms Jun 2023Heterotrophic nitrification-aerobic denitrification (HN-AD) is an efficient nitrogen removal process and the genus is one important group of the HN-AD bacteria. During...
Three Novel Marine Species of , sp. nov., sp. nov. and sp. nov., and the Characterization of Their Capability to Perform Heterotrophic Nitrification and Aerobic Denitrification.
Heterotrophic nitrification-aerobic denitrification (HN-AD) is an efficient nitrogen removal process and the genus is one important group of the HN-AD bacteria. During an investigation of the microbial diversity in marine ranching of the Pearl River Estuary (PR China), three bacterial strains, designated SCSIO 75817, SCSIO 76264 and SCSIO 80058, were isolated from sediments. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the three strains belonged to the genus and their closest neighbors were DSM 22220 (97.6-98.0%), . CGMCC 1.13898 (97.3-97.6%) and . MCCC 1A16381 (97.1-97.4%), respectively. The analysis results of 16S rRNA gene similarity, ANI, AAI and dDDH showed that the pairwise similarities between these three strains and their closest neighbors were 97.4-98.5%, 76.9-81.0%, 75.5-79.6% and 20.3-23.3%, respectively. Polyphasic taxonomic data of the phylogenetic, phenotypic and chemotaxonomic analyses indicate that these strains represent three novel species in the genus , for which the names sp. nov., sp. nov. and sp. nov. are proposed, respectively. The study also demonstrated the heterotrophic nitrification-aerobic denitrification (HN-AD) ability of the novel species SCSIO 75817. When it was aerobically cultivated at 28 °C using NH-N, NO-N and NO-N as the sole nitrogen sources, the nitrogen removal efficiencies were 73.4, 55.27 and 49.2%, respectively, and the maximum removal rates were 3.05, 1.82 and 1.63 mg/L/h, respectively. The results suggest that it has promising potential for wastewater treatment.
PubMed: 37375034
DOI: 10.3390/microorganisms11061532 -
Applied and Environmental Microbiology Jul 2023Metabolic degeneracy describes the phenomenon that cells can use one substrate through different metabolic routes, while metabolic plasticity, refers to the ability of...
Functional Degeneracy in Paracoccus denitrificans Pd1222 Is Coordinated via RamB, Which Links Expression of the Glyoxylate Cycle to Activity of the Ethylmalonyl-CoA Pathway.
Metabolic degeneracy describes the phenomenon that cells can use one substrate through different metabolic routes, while metabolic plasticity, refers to the ability of an organism to dynamically rewire its metabolism in response to changing physiological needs. A prime example for both phenomena is the dynamic switch between two alternative and seemingly degenerate acetyl-CoA assimilation routes in the alphaproteobacterium Paracoccus denitrificans Pd1222: the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). The EMCP and the GC each tightly control the balance between catabolism and anabolism by shifting flux away from the oxidation of acetyl-CoA in the tricarboxylic acid (TCA) cycle toward biomass formation. However, the simultaneous presence of both the EMCP and GC in P. denitrificans Pd1222 raises the question of how this apparent functional degeneracy is globally coordinated during growth. Here, we show that RamB, a transcription factor of the ScfR family, controls expression of the GC in P. denitrificans Pd1222. Combining genetic, molecular biological and biochemical approaches, we identify the binding motif of RamB and demonstrate that CoA-thioester intermediates of the EMCP directly bind to the protein. Overall, our study shows that the EMCP and the GC are metabolically and genetically linked with each other, demonstrating a thus far undescribed bacterial strategy to achieve metabolic plasticity, in which one seemingly degenerate metabolic pathway directly drives expression of the other. Carbon metabolism provides organisms with energy and building blocks for cellular functions and growth. The tight regulation between degradation and assimilation of carbon substrates is central for optimal growth. Understanding the underlying mechanisms of metabolic control in bacteria is of importance for applications in health (e.g., targeting of metabolic pathways with new antibiotics, development of resistances) and biotechnology (e.g., metabolic engineering, introduction of new-to-nature pathways). In this study, we use the alphaproteobacterium P. denitrificans as model organism to study functional degeneracy, a well-known phenomenon of bacteria to use the same carbon source through two different (competing) metabolic routes. We demonstrate that two seemingly degenerate central carbon metabolic pathways are metabolically and genetically linked with each other, which allows the organism to control the switch between them in a coordinated manner during growth. Our study elucidates the molecular basis of metabolic plasticity in central carbon metabolism, which improves our understanding of how bacterial metabolism is able to partition fluxes between anabolism and catabolism.
Topics: Acetyl Coenzyme A; Paracoccus denitrificans; Bacterial Proteins; Carbon; Glyoxylates
PubMed: 37318336
DOI: 10.1128/aem.00238-23