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1.
Sci Rep ; 13(1): 99, 2023 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-36596824

RESUMO

Fermentation of dietary fiber by gut microbes produces short-chain fatty acids (SCFA), but fermentation outcomes are affected by dietary fiber source and microbiota composition. The aim of this study was to investigate the effect of two different fecal microbial compositions on in vitro fermentation of a standardized amount of oat, rye, and wheat breads. Two human fecal donors with different microbial community composition were recruited. Bread samples were digested enzymatically. An in vitro fermentation model was used to study SCFA production, dietary fiber degradation, pH, and changes in microbiota. Feces from donor I had high relative abundance of Bacteroides and Escherichia/Shigella, whereas feces from donor II were high in Prevotella and Subdoligranulum. Shifts in microbiota composition were observed during fermentation. SCFA levels were low in the samples with fecal microbiota from donor I after 8 h of fermentation, but after 24 h acetate and propionate levels were similar in the samples from the different donors. Butyrate levels were higher in the fermentation samples from donor II, especially with rye substrate, where high abundance of Subdoligranulum was observed. Dietary fiber degradation was also higher in the fermentation samples from donor II. In conclusion, fermentation capacity and substrate utilization differed between the two different microbiota compositions.


Assuntos
Microbiota , Triticum , Humanos , Triticum/metabolismo , Pão , Secale/metabolismo , Avena/metabolismo , Fermentação , Ácidos Graxos Voláteis/metabolismo , Fezes/química , Fibras na Dieta/metabolismo
2.
Nutrients ; 15(2)2023 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-36678320

RESUMO

Essential oils (EO) are promising feed additives for their antibacterial, antioxidant, and immune-enhancing abilities with low toxicity. Carvacrol, thymol, and cinnamaldehyde are commonly used to synthesize EO. However, few studies focus on combining these three EO in early-weaned piglets. In the present study, 24 piglets weaned at 21 d of age were randomly divided into 2 groups (6 replicate pens per group, 2 piglets per pen). The piglets were fed a basal diet (the control group) and a basal diet supplemented with 400 mg/kg EO (a blend consisting of carvacrol, thymol, and cinnamaldehyde, the EO group) for 28 days. At the end of the experiment, one piglet per pen was randomly chosen to be sacrificed. Growth performance, hematology, plasma biochemical indices, antioxidant capacity, intestinal epithelial development and immunity, colonic volatile fatty acids (VFA), and microbiota were determined. The results indicated that the diet supplemented with EO significantly improved average daily feed intake (ADFI, p < 0.01) and average daily gain (ADG, p < 0.05) in the day 0 to 28 period. EO supplementation led to a significant decrease in plasma lysozyme (p < 0.05) and cortisol levels (p < 0.01). Additionally, EO significantly promoted jejunal goblet cells in the villus, jejunal mucosa ZO-1 mRNA expression, ileal villus height, and ileal villus height/crypt depth ratio in piglets (p < 0.05). The ileal mucosal TLR4 and NFκB p-p65/p65 protein expression were significantly inhibited in the EO group (p < 0.05). Colonic digesta microbiota analysis revealed that bacteria involving the Erysipelotrichaceae family, Holdemanella genus, Phascolarctobacterium genus, and Vibrio genus were enriched in the EO group. In conclusion, these findings indicate that the EO blend improves ADG and ADFI in the day 0 to 28 period, as well as intestinal epithelial development and intestinal immunity in early-weaned piglets, which provides a theoretical basis for the combined use of EO in weaned piglets.


Assuntos
Microbiota , Óleos Voláteis , Animais , Suínos , Antioxidantes/farmacologia , Antioxidantes/metabolismo , Óleos Voláteis/farmacologia , Timol/farmacologia , Suplementos Nutricionais
3.
Sensors (Basel) ; 23(2)2023 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-36679633

RESUMO

The study of the human microbiome is a multidisciplinary area ranging from the field of technology to that of personalized medicine. The possibility of using microbiota biomarkers to improve the diagnosis and monitoring of diseases (e.g., cancer), health conditions (e.g., obesity) or relevant processes (e.g., aging) has raised great expectations, also in the field of bioelectroanalytical chemistry. The well-known advantages of electrochemical biosensors-high sensitivity, fast response, and the possibility of miniaturization, together with the potential for new nanomaterials to improve their design and performance-position them as unique tools to provide a better understanding of the entities of the human microbiome and raise the prospect of huge and important developments in the coming years. This review article compiles recent applications of electrochemical (bio)sensors for monitoring microbial metabolites and disease biomarkers related to different types of human microbiome, with a special focus on the gastrointestinal microbiome. Examples of electrochemical devices applied to real samples are critically discussed, as well as challenges to be faced and where future developments are expected to go.


Assuntos
Técnicas Biossensoriais , Microbiota , Nanoestruturas , Humanos , Técnicas Eletroquímicas/métodos , Biomarcadores , Técnicas Biossensoriais/métodos
4.
Gut Microbes ; 15(1): 2145845, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36691230

RESUMO

Mounting evidence suggests that acute appendicitis (AA) is not one but two diseases: complicated appendicitis, which is associated with necrosis leading to perforation or periappendicular abscess, and uncomplicated appendicitis, which does not necessarily result in perforation. Even though AA is the most frequent cause of surgery from abdominal pain, little is known about the origins and etiopathogenesis of this disease, much less regarding the different disease types. In this study, we investigated the microbiome (inter-domain amplicon and metagenome sequencing) of samples from the appendix, rectum and peritoneum of 60 children and adolescents with AA to assess the composition and potential function of bacteria, archaea and fungi. The analysis of the appendix microbial community revealed a shift depending on the severity of the AA. This shift was reflected by two major community state types that represented the complicated and uncomplicated cases. We could demonstrate that complicated, but not uncomplicated, appendicitis is associated with a significant local expansion of oral, bacterial pathogens in the appendix, most strongly influenced by necrotizing Fusobacterium spp., Porphyromonas and Parvimonas. Uncomplicated appendicitis, however, was characterized by gut-associated microbiomes. Our findings support the hypothesis that two disease types exist in AA, which cannot be distinguished beyond doubt using standard clinical characterization methods or by analysis of the patient's rectal microbiome. An advanced microbiome diagnosis, however, could improve non-surgical treatment of uncomplicated AA.


Assuntos
Apendicite , Apêndice , Microbioma Gastrointestinal , Microbiota , Criança , Adolescente , Humanos , Apendicite/tratamento farmacológico , Apendicite/patologia , Apendicite/cirurgia , Apêndice/microbiologia , Apêndice/patologia , Bactérias , Doença Aguda
5.
J Hazard Mater ; 446: 130646, 2023 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-36587599

RESUMO

Earthworm intestinal bacteria and indigenous soil bacteria work closely during various biochemical processes and play a crucial role in maintaining the internal stability of the soil environment. However, the response mechanism of these bacterial communities to external pesticide disturbance is unknown. In this study, soil and earthworm gut contents were metagenomically sequenced after exposure to various concentrations of nitrochlorobenzene (0-1026.7 mg kg-1). A high degree of similarity was found between the microbial community composition and abundance in the worm gut and soil, both of which decreased significantly (P < 0.05) under elevated pesticide stress. The toxicity sharing model (TSM) showed that the toxicity sharing capacity was 97.4-125.7 % and 100.4-130.2 % for Egenes (genes in the worm gut) and Emet(degradation genes in the worm gut) in the earthworm intestinal microbiome, respectively. This indicated that the earthworm intestinal microbiome assisted in relieving the pesticide toxicity of the indigenous soil microbiome. This study showed that the TSM could quantitatively describe the toxic effect of pesticides on the earthworm intestinal microbiome. It provides a new analytical model for investigating the ecological alliance between earthworm intestinal microbiome and indigenous soil microbiome under pesticide stress while contributing a more profound understanding of the potential to use earthworms to mitigate pesticide pollution in soils and develop earthworm-based soil remediation techniques.


Assuntos
Microbioma Gastrointestinal , Microbiota , Oligoquetos , Praguicidas , Poluentes do Solo , Animais , Microbioma Gastrointestinal/genética , Oligoquetos/genética , Oligoquetos/microbiologia , Praguicidas/toxicidade , Bactérias/genética , Solo/química , Poluentes do Solo/análise
6.
J Hazard Mater ; 446: 130714, 2023 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-36599276

RESUMO

Recently, biodegradable plastics (BPs) are emerging as a sustainable alternative to traditional plastics. When released into an aquatic environment, the biodegradable performance of BPs is influenced by biochemical processes, especially the developed plastisphere. However, studies addressing the biodegrading capacity of BPs and traditional plastics within the plastisphere are still limited. Here, we investigated plastisphere community variations and their capacity to biodegrade polyethylene terephthalate (PET) and starch-based plastics (SBP) for four time periods (15, 30, 45, and 80 days) in three freshwaters. Unexpectedly, there is no significant difference in the microbial communities and network structure of the plastisphere between SBP and PET. Moreover, SBP tended to age rapidly at the early stage (0-15 days), while the aging degree of SBP and PET did not display an obvious difference at 80 days. Partial least squares path modeling suggested that plastic aging was mainly dominated by keystone taxa of network and aquatic environmental factors. These results suggest that the aging rate of commercial BPs may not be as fast as we imagine in freshwaters (SBP ≈ PET), and the environmental behaviors of BPs in the aquatic environment should be paid more attention to.


Assuntos
Plásticos Biodegradáveis , Microbiota , Plásticos , Água Doce
7.
J Hazard Mater ; 446: 130707, 2023 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-36603428

RESUMO

Biotransformation mediated by microbes can affect the biogeochemical cycle of arsenic. However, arsenic biotransformation mediated by earthworm-related microorganisms has not been well explored, especially the role played by earthworm skin microbiota. Herein, we reveal the profiles of arsenic biotransformation genes (ABGs) and elucidate the microbial communities of the earthworm gut, skin, and surrounding soil from five different soil environments in China. The relative abundance of ABGs in the earthworm skin microbiota, which were dominated by genes associated with arsenate reduction and transport, was approximately three times higher than that in the surrounding soil and earthworm gut microbiota. The composition and diversity of earthworm skin microbiota differed significantly from those of the soil and earthworm gut, comprising a core bacterial community with a relative abundance of 96% Firmicutes and a fungal community with relative abundances of 50% Ascomycota and 13% Mucoromycota. In addition, stochastic processes mainly contributed to the microbial community assembly across all samples. Moreover, fungal genera such as Vishniacozyma and Oomyces were important mediators of ABGs involved in the biogeochemical cycle of arsenic. This is the first study to investigate earthworm skin as a reservoir of microbial diversity in arsenic biotransformation. Our findings broaden the current scientific knowledge of the involvement of earthworms in the arsenic biogeochemical cycle.


Assuntos
Arsênio , Microbiota , Oligoquetos , Animais , Arsênio/metabolismo , Oligoquetos/metabolismo , Biotransformação , Solo/química , Microbiologia do Solo
8.
PLoS Comput Biol ; 19(1): e1010820, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36608142

RESUMO

In recent years, unsupervised analysis of microbiome data, such as microbial network analysis and clustering, has increased in popularity. Many new statistical and computational methods have been proposed for these tasks. This multiplicity of analysis strategies poses a challenge for researchers, who are often unsure which method(s) to use and might be tempted to try different methods on their dataset to look for the "best" ones. However, if only the best results are selectively reported, this may cause over-optimism: the "best" method is overly fitted to the specific dataset, and the results might be non-replicable on validation data. Such effects will ultimately hinder research progress. Yet so far, these topics have been given little attention in the context of unsupervised microbiome analysis. In our illustrative study, we aim to quantify over-optimism effects in this context. We model the approach of a hypothetical microbiome researcher who undertakes four unsupervised research tasks: clustering of bacterial genera, hub detection in microbial networks, differential microbial network analysis, and clustering of samples. While these tasks are unsupervised, the researcher might still have certain expectations as to what constitutes interesting results. We translate these expectations into concrete evaluation criteria that the hypothetical researcher might want to optimize. We then randomly split an exemplary dataset from the American Gut Project into discovery and validation sets multiple times. For each research task, multiple method combinations (e.g., methods for data normalization, network generation, and/or clustering) are tried on the discovery data, and the combination that yields the best result according to the evaluation criterion is chosen. While the hypothetical researcher might only report this result, we also apply the "best" method combination to the validation dataset. The results are then compared between discovery and validation data. In all four research tasks, there are notable over-optimism effects; the results on the validation data set are worse compared to the discovery data, averaged over multiple random splits into discovery/validation data. Our study thus highlights the importance of validation and replication in microbiome analysis to obtain reliable results and demonstrates that the issue of over-optimism goes beyond the context of statistical testing and fishing for significance.


Assuntos
Microbiota , Aprendizado de Máquina , Consórcios Microbianos , Bactérias , Análise por Conglomerados
9.
J Hazard Mater ; 446: 130712, 2023 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-36621296

RESUMO

With the intensification of microplastic (MP) pollution, the impact of MPs on soil ecosystems has garnered considerable attention. We investigated the effects of two commonly used MPs, polyethylene (PE) and polypropylene (PP), at different sizes and doses, on the properties and microbial communities in saline-alkali soil. We found that MP treatment significantly reduced the electrical conductivity but somewhat enhanced the enzyme activities and effective nutrient content of the soil. Microbial diversity is affected by the type, dose, size and interaction of MPs, with fungi being more sensitive than bacteria. Under high-dose PE treatment, the dominant bacteria and fungi enriched, and the diversity indexes declined significantly. Meanwhile, under high-dose PP treatment, several unique bacteria and fungi with low abundance were observed, which eventually increased the diversity indexes. Moreover, PE exerted a stronger effect on bacterial function than PP. High-dose PE treatment suppressed the nitrogen fixation potential of soil bacteria. However, high-dose PP treatment promoted that. In conclusion, our findings showed that PE exerts a stronger negative effect on saline-alkali soil ecosystems than PP. Our findings help bridge the knowledge gap in the impact of MPs on saline-alkaline soils and provide guidance for the rational use of agricultural plastics in saline-alkaline soils.


Assuntos
Microbiota , Poluentes do Solo , Microplásticos/farmacologia , Plásticos , Solo , Álcalis , Microbiologia do Solo , Poluentes do Solo/análise , Polipropilenos , Polietileno/farmacologia , Bactérias
10.
Biotechniques ; 74(1): 9-21, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36601888

RESUMO

Butyrate and propionate represent two of three main short-chain fatty acids produced by the intestinal microbiota. In healthy populations, their levels are reportedly equimolar, whereas a deviation in their ratio has been observed in various diseased cohorts. Monitoring such a ratio represents a valuable metric; however, it remains a challenge to adopt short-chain fatty acid detection techniques in clinical settings because of the volatile nature of these acids. Here we aimed to estimate short-chain fatty acid information indirectly through a novel, simple quantitative PCR-compatible assay (liquid array diagnostics) targeting a limited number of microbiome 16S markers. Utilizing 15 liquid array diagnostics probes to target microbiome markers selected by a model that combines partial least squares and linear discriminant analysis, the classes (normal vs high propionate-to-butyrate ratio) separated at a threshold of 2.6 with a prediction accuracy of 96%.


Assuntos
Butiratos , Microbiota , Propionatos , RNA Ribossômico 16S/genética , Ácidos Graxos Voláteis/análise , Bactérias/genética
11.
Chemosphere ; 316: 137775, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-36621691

RESUMO

The quality and quantity of domestic sewage discharge vary significantly during the Chinese Spring Festival due to the huge population shift. The dynamics of microbial community traits during the Spring Festival, particularly the phylogenetic group-based assembly and co-occurrence patterns, are however little understood. Here, influent and activated sludge samples from 2 full-scale wastewater treatment plants were collected bi-daily throughout a 20-day Spring Festival period and subjected to high-throughput Illumina-MiSeq sequencing. The findings revealed that the microbial communities in the activated sludge displayed a comparatively stable pattern, and that the influent communities experienced significant temporal fluctuations in terms of diversity and composition. The characterization by "Infer Community Assembly Mechanisms by Phylogenetic-bin based null model" demonstrated that for Competibacter glycogen-accumulating organisms, the assembly mechanism shifted from deterministic process (HoS = 69.5%) before the Spring Festival to stochastic process (DR = 65.9%) after the Spring Festival. The network analysis revealed that the network structure of sludge communities was more stable before the Spring Festival than that after the Spring Festival. Additionally, sludge communities had no keystone species in common with the influent before the Spring Festival, while the sludge and influent communities shared two keystone taxa after the Spring Festival (Sebaldella and Candidatus Competibacter). This study would deepen our understanding of the microbial ecology in biological wastewater treatment systems, which also aids in managing wastewater treatment plants.


Assuntos
Gammaproteobacteria , Microbiota , Purificação da Água , Esgotos , Filogenia , Férias e Feriados , Reatores Biológicos
12.
Chemosphere ; 316: 137786, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-36634716

RESUMO

The by-product from the anaerobic digestion of food waste (FW) called the digestate (DFW) needs proper disposal because of its high environmental burden. Composting can transform DFW into a nutrient-containing soil improver via a series of microbial metabolic activities. However, the long composting time and high amount of ammonia emission are the key concerns of DFW composting. In the present study, the effect of DFW-derived biochar (BC-DFW) on microbial succession and its involvement in nitrogen transformation and humification during DFW composting were investigated. The results indicated that the BC-DFW accelerated bacterial and fungal evolution, and the bacterial diversity was augmented by increasing the amount of BC-DFW. In particular, Cryomorpha, Castellaniella, Aequorivita, and Moheibacter were enriched by the addition of BC-DFW, thereby enhancing the degradation of organic matter and nitrogen transformation and increasing the germination index. The group with 25% BC-DFW contained a higher relative abundance of Cryomorpha (2.08%, 2.47%) than the control (0.39%, 1.72%) on days 19 and 35 which benefited the degradation of organic matter. The group with 25% BC-DFW quickly enhanced the growth of Nitrosomonas, thereby accelerating the conversion of ammonium-nitrogen to nitrate-nitrogen and reducing the phytotoxicity of the composting product.


Assuntos
Compostagem , Microbiota , Eliminação de Resíduos , Alimentos , Solo , Nitrogênio , Esterco
13.
Nature ; 613(7945): 639-649, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36697862

RESUMO

Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.


Assuntos
Microbiota , Placenta , Gravidez , Feminino , Animais , Humanos , Biomassa , Placenta/microbiologia , Microbiota/genética , Líquido Amniótico/microbiologia , Cuidado Pré-Natal , Mamíferos
14.
Brief Bioinform ; 24(1)2023 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-36617187

RESUMO

Differential abundance analysis (DAA) is one central statistical task in microbiome data analysis. A robust and powerful DAA tool can help identify highly confident microbial candidates for further biological validation. Current microbiome studies frequently generate correlated samples from different microbiome sampling schemes such as spatial and temporal sampling. In the past decade, a number of DAA tools for correlated microbiome data (DAA-c) have been proposed. Disturbingly, different DAA-c tools could sometimes produce quite discordant results. To recommend the best practice to the field, we performed the first comprehensive evaluation of existing DAA-c tools using real data-based simulations. Overall, the linear model-based methods LinDA, MaAsLin2 and LDM are more robust than methods based on generalized linear models. The LinDA method is the only method that maintains reasonable performance in the presence of strong compositional effects.


Assuntos
Benchmarking , Microbiota , Antivirais , Microbiota/genética , Modelos Lineares , Bases de Dados Factuais , Metagenômica/métodos
15.
Water Res ; 230: 119575, 2023 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-36623385

RESUMO

While dam construction supports social and economic development, changes in hydraulic conditions can also affect natural aquatic ecosystems, especially microbial ecosystems. The compositional and functional traits of multi-trophic microbiota can be altered by dam construction, which may result in changes in aquatic predator-prey interactions. To understand this process, we performed a large-scale sampling campaign in the urban reaches of the dam-impacted Yangtze River (1 995 km) and obtained 211 metagenomic datasets and water quality data. We first compared the compositional traits of planktonic microbial communities upstream, downstream, and in a dam reservoir. Results showed that Bacteroidetes (R-strategy) bacteria were more likely to survive upstream, whilst the reservoir and downstream regions were more conducive to the survival of K-strategy bacteria such as Actinobacteria. Eukaryotic predators tended to be enriched upstream, whilst phototrophs tended to be enriched in the reservoir and downstream regions. Based on bipartite networks, we inferred that the potential microbial predator-prey interactions gradually and significantly decreased from upstream to the downstream and dam regions, affecting 56% of keystone microbial species. Remarkably, functional analysis showed that the abundance of the photosynthetic gene psbO was higher in the reservoir and downstream regions, whilst the abundance of the KEGG carbohydrate metabolic pathway was higher upstream. These results indicate that dam construction in the Yangtze River induced planktonic microbial ecosystem transformation from detritus-based food webs to autotroph-based food webs.


Assuntos
Microbiota , Plâncton , Ecossistema , Rios/microbiologia , Cadeia Alimentar , Bacteroidetes , China
16.
Brief Bioinform ; 24(1)2023 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-36631408

RESUMO

The gut microbial communities are highly plastic throughout life, and the human gut microbial communities show spatial-temporal dynamic patterns at different life stages. However, the underlying association between gut microbial communities and time-related factors remains unclear. The lack of context-awareness, insufficient data, and the existence of batch effect are the three major issues, making the life trajection of the host based on gut microbial communities problematic. Here, we used a novel computational approach (microDELTA, microbial-based deep life trajectory) to track longitudinal human gut microbial communities' alterations, which employs transfer learning for context-aware mining of gut microbial community dynamics at different life stages. Using an infant cohort, we demonstrated that microDELTA outperformed Neural Network for accurately predicting the age of infant with different delivery mode, especially for newborn infants of vaginal delivery with the area under the receiver operating characteristic curve of microDELTA and Neural Network at 0.811 and 0.436, respectively. In this context, we have discovered the influence of delivery mode on infant gut microbial communities. Along the human lifespan, we also applied microDELTA to a Chinese traveler cohort, a Hadza hunter-gatherer cohort and an elderly cohort. Results revealed the association between long-term dietary shifts during travel and adult gut microbial communities, the seasonal cycling of gut microbial communities for the Hadza hunter-gatherers, and the distinctive microbial pattern of elderly gut microbial communities. In summary, microDELTA can largely solve the issues in tracing the life trajectory of the human microbial communities and generate accurate and flexible models for a broad spectrum of microbial-based longitudinal researches.


Assuntos
Aprendizado Profundo , Microbioma Gastrointestinal , Microbiota , Recém-Nascido , Lactente , Feminino , Humanos , Idoso , Dieta
17.
Nat Ecol Evol ; 7(1): 143-154, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36593292

RESUMO

Species interactions drive evolution while evolution shapes these interactions. The resulting eco-evolutionary dynamics and their repeatability depend on how adaptive mutations available to community members affect fitness and ecologically relevant traits. However, the diversity of adaptive mutations is not well characterized, and we do not know how this diversity is affected by the ecological milieu. Here we use barcode lineage tracking to address this question in a community of yeast Saccharomyces cerevisiae and alga Chlamydomonas reinhardtii that have a net commensal relationship that results from a balance between competitive and mutualistic interactions. We find that yeast has access to many adaptive mutations with diverse ecological consequences, in particular those that increase and reduce the yields of both species. The presence of the alga does not change which mutations are adaptive in yeast (that is, there is no fitness trade-off for yeast between growing alone or with alga), but rather shifts selection to favour yeast mutants that increase the yields of both species and make the mutualism stronger. Thus, in the presence of the alga, adaptative mutations contending for fixation in yeast are more likely to enhance the mutualism, even though cooperativity is not directly favoured by natural selection in our system. Our results demonstrate that ecological interactions not only alter the trajectory of evolution but also dictate its repeatability; in particular, weak mutualisms can repeatably evolve to become stronger.


Assuntos
Evolução Biológica , Chlamydomonas reinhardtii , Microbiota , Saccharomyces cerevisiae , Simbiose , Microbiota/genética , Microbiota/fisiologia , Mutação , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/fisiologia , Simbiose/genética , Simbiose/fisiologia , Chlamydomonas reinhardtii/genética , Chlamydomonas reinhardtii/fisiologia
18.
Appl Microbiol Biotechnol ; 107(2-3): 955-969, 2023 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-36625913

RESUMO

1,4-Dioxane is a contaminant of emerging concern that has been commonly detected in groundwater. In this study, a stable and robust 1,4-dioxane degrading enrichment culture was obtained from uncontaminated soil. The enrichment was capable to metabolically degrade 1,4-dioxane at both high (100 mg L-1) and environmentally relevant concentrations (300 µg L-1), with a maximum specific 1,4-dioxane degradation rate (qmax) of 0.044 ± 0.001 mg dioxane h-1 mg protein-1, and 1,4-dioxane half-velocity constant (Ks) of 25 ± 1.6 mg L-1. The microbial community structure analysis suggested Pseudonocardia species, which utilize the dioxane monooxygenase for metabolic 1,4-dioxane biodegradation, were the main functional species for 1,4-dioxane degradation. The enrichment culture can adapt to both acidic (pH 5.5) and alkaline (pH 8) conditions and can recover degradation from low temperature (10°C) and anoxic (DO < 0.5 mg L-1) conditions. 1,4-Dioxane degradation of the enrichment culture was reversibly inhibited by TCE with concentrations higher than 5 mg L-1 and was completely inhibited by the presence of 1,1-DCE as low as 1 mg L-1. Collectively, these results demonstrated indigenous stable and robust 1,4-dioxane degrading enrichment culture can be obtained from uncontaminated sources and can be a potential candidate for 1,4-dioxane bioaugmentation at environmentally relevant conditions. KEY POINTS: •1,4-Dioxane degrading enrichment was obtained from uncontaminated soil. • The enrichment culture could degrade 1,4-dioxane to below 10 µg L-1. •Low Ks and low cell yield of the enrichment benefit its application in bioremediation.


Assuntos
Microbiota , Poluentes Químicos da Água , Solo , Biodegradação Ambiental , Dioxanos/metabolismo , Poluentes Químicos da Água/metabolismo
19.
Huan Jing Ke Xue ; 44(1): 262-271, 2023 Jan 08.
Artigo em Chinês | MEDLINE | ID: mdl-36635814

RESUMO

In recent years, the ecosystems on the Qinghai-Tibet Plateau (QTP) have been facing a high risk of degradation due to the impacts of climate change and human activities. As one of the important components in river ecosystems, microbial communities can reflect the overall changes in the watershed and are regarded as indicators of the health of river ecosystems. In order to investigate the diversity and composition characteristics of bacterial communities in river ecosystems on the QTP, 65 samples were collected from the Yellow River, Yangtze River, Lancang River, Nujiang River, Yarlung Tsangpo River, and Qaidam Basin on the QTP in July 2021 and were analyzed using 16S rRNA high-throughput sequencing. The results showed that the detected bacterial communities covered 65 phyla and 1311 genera in total. Bacterial communities had high α-diversity indexes across the rivers, indicating that the bacterial richness and diversity in rivers on the QTP were at a high level. Among them, Chao and observed OTUs had significantly negative relationships with SRP/TP. The dominant phyla were Proteobacteria, Bacteroidota, Actinobacteriota, and Cyanobacteria. The dominant classes were γ-proteobacteria, Bacteroidia, and α-proteobacteria. The dominant genera were Flavobacterium and Limnohabitans. The results of principal coordinate analysis and permutational MANOVA suggested significant differences in bacterial community structure among the rivers on the QTP. Canonical correspondence analysis showed that the significant environmental variables associated with the variation in the bacterial communities were physicochemical properties of the river water, including conductivity, pH, dissolved silicon, and dissolved organic carbon, as well as watershed characteristics, including the average normalized differential vegetation index, average slope, cumulative water channel distance, catchment size, proportion of shrub area, and average elevation. Among them, conductivity had the strongest influence on bacteria distribution on the QTP. These results provide a database and information for understanding the composition characteristics of microbial communities on the QTP and identifying environmental factors influencing the diversity of bacteria communities.


Assuntos
Microbiota , Rios , Bactérias/genética , Bacteroidetes , Genes de RNAr , Rios/microbiologia , RNA Ribossômico 16S/genética , Tibet
20.
Gut Microbes ; 15(1): 2166780, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36656562

RESUMO

Visceral hypersensitivity, a fundamental mechanism of chronic visceral pain disorders, can result from both central or peripheral factors, or their combination. As an important regulator of normal gut function, the gut microbiota has been implicated as a key peripheral factor in the pathophysiology of visceral hypersensitivity. Patients with chronic gastrointestinal disorders, such as irritable bowel syndrome, often present with abdominal pain secondary to adverse reactions to dietary components. As both long- and short-term diets are major determinants of gut microbiota configuration that can result in changes in microbial metabolic output, it is becoming increasingly recognized that diet-microbiota interactions play an important role in the genesis of visceral sensitivity. Changes in pain signaling may occur via diet-induced changes in secretion of mediators by both the microbiota and/or host cells. This review will examine the peripheral influence of diet-microbiota interactions underlying increased visceral sensitivity.


Assuntos
Microbioma Gastrointestinal , Síndrome do Intestino Irritável , Microbiota , Humanos , Microbioma Gastrointestinal/fisiologia , Dieta , Percepção
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