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1.
PLoS One ; 19(5): e0284642, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38718041

RESUMO

The GO DNA repair system protects against GC → TA mutations by finding and removing oxidized guanine. The system is mechanistically well understood but its origins are unknown. We searched metagenomes and abundantly found the genes encoding GO DNA repair at the Lost City Hydrothermal Field (LCHF). We recombinantly expressed the final enzyme in the system to show MutY homologs function to suppress mutations. Microbes at the LCHF thrive without sunlight, fueled by the products of geochemical transformations of seafloor rocks, under conditions believed to resemble a young Earth. High levels of the reductant H2 and low levels of O2 in this environment raise the question, why are resident microbes equipped to repair damage caused by oxidative stress? MutY genes could be assigned to metagenome-assembled genomes (MAGs), and thereby associate GO DNA repair with metabolic pathways that generate reactive oxygen, nitrogen and sulfur species. Our results indicate that cell-based life was under evolutionary pressure to cope with oxidized guanine well before O2 levels rose following the great oxidation event.


Assuntos
Reparo do DNA , Guanina , Metagenoma , Oxirredução , Guanina/metabolismo , Fontes Hidrotermais/microbiologia
2.
Sci Data ; 11(1): 484, 2024 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-38730026

RESUMO

Barley (Hordeum vulgare) is essential to global food systems and the brewing industry. Its physiological traits and microbial communities determine malt quality. Although microbes influence barley from seed health to fermentation, there is a gap in metagenomic insights during seed storage. Crucially, elucidating the changes in microbial composition associated with barley seeds is imperative for understanding how these fluctuations can impact seed health and ultimately, influence both agricultural yield and quality of barley-derived products. Whole metagenomes were sequenced from eight barley seed samples obtained at different storage time points from harvest to nine months. After binning, 82 metagenome-assembled genomes (MAGs) belonging to 26 distinct bacterial genera were assembled, with a substantial proportion of potential novel species. Most of our MAG dataset (61%) showed over 90% genome completeness. This pioneering barley seed microbial genome retrieval provides insights into species diversity and structure, laying the groundwork for understanding barley seed microbiome interactions at the genome level.


Assuntos
Hordeum , Sementes , Hordeum/microbiologia , Hordeum/genética , Sementes/microbiologia , Metagenoma , Microbiota , Metagenômica , Genoma Microbiano , Genoma Bacteriano , Bactérias/genética , Bactérias/classificação
3.
Sci Rep ; 14(1): 10540, 2024 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-38719945

RESUMO

Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea.


Assuntos
Bacteriófagos , Bivalves , Brânquias , Metagenômica , Animais , Metagenômica/métodos , Bacteriófagos/genética , Bacteriófagos/isolamento & purificação , Brânquias/microbiologia , Brânquias/virologia , Brânquias/metabolismo , Bivalves/microbiologia , Bivalves/virologia , Bivalves/genética , Perfilação da Expressão Gênica , Transcriptoma , Viroma/genética , Bactérias/genética , Bactérias/classificação , Simbiose/genética , Metagenoma
4.
Sci Rep ; 14(1): 10525, 2024 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-38720057

RESUMO

The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.


Assuntos
Arachis , Bactérias , Metagenômica , Microbiota , RNA Ribossômico 16S , Rizosfera , Microbiologia do Solo , Arachis/microbiologia , Índia , Microbiota/genética , RNA Ribossômico 16S/genética , Metagenômica/métodos , Bactérias/genética , Bactérias/classificação , Bactérias/isolamento & purificação , Fazendas , Raízes de Plantas/microbiologia , Filogenia , Metagenoma , Biodiversidade
5.
Microbiome ; 12(1): 82, 2024 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-38725064

RESUMO

BACKGROUND: The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined. RESULTS: Leveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR-Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that the viruses in the rumen may regulate microbes at strain and community levels through both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions. CONCLUSIONS: These findings provide a substantive framework for further investigations to unravel the functional roles of the virome in the rumen in shaping the microbiome and influencing overall animal production performance. Video Abstract.


Assuntos
Metagenoma , Rúmen , Vírus , Rúmen/microbiologia , Rúmen/virologia , Animais , Vírus/classificação , Vírus/genética , Microbioma Gastrointestinal , Viroma , Ruminantes/microbiologia , Ruminantes/virologia , Metano/metabolismo , Ração Animal , Bactérias/classificação , Bactérias/genética
6.
Microbiome ; 12(1): 91, 2024 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-38760842

RESUMO

BACKGROUND: Dark pigmented snow and glacier ice algae on glaciers and ice sheets contribute to accelerating melt. The biological controls on these algae, particularly the role of viruses, remain poorly understood. Giant viruses, classified under the nucleocytoplasmic large DNA viruses (NCLDV) supergroup (phylum Nucleocytoviricota), are diverse and globally distributed. NCLDVs are known to infect eukaryotic cells in marine and freshwater environments, providing a biological control on the algal population in these ecosystems. However, there is very limited information on the diversity and ecosystem function of NCLDVs in terrestrial icy habitats. RESULTS: In this study, we investigate for the first time giant viruses and their host connections on ice and snow habitats, such as cryoconite, dark ice, ice core, red and green snow, and genomic assemblies of five cultivated Chlorophyta snow algae. Giant virus marker genes were present in almost all samples; the highest abundances were recovered from red snow and the snow algae genomic assemblies, followed by green snow and dark ice. The variety of active algae and protists in these GrIS habitats containing NCLDV marker genes suggests that infection can occur on a range of eukaryotic hosts. Metagenomic data from red and green snow contained evidence of giant virus metagenome-assembled genomes from the orders Imitervirales, Asfuvirales, and Algavirales. CONCLUSION: Our study highlights NCLDV family signatures in snow and ice samples from the Greenland ice sheet. Giant virus metagenome-assembled genomes (GVMAGs) were found in red snow samples, and related NCLDV marker genes were identified for the first time in snow algal culture genomic assemblies; implying a relationship between the NCLDVs and snow algae. Metatranscriptomic viral genes also aligned with metagenomic sequences, suggesting that NCLDVs are an active component of the microbial community and are potential "top-down" controls of the eukaryotic algal and protistan members. This study reveals the unprecedented presence of a diverse community of NCLDVs in a variety of glacial habitats dominated by algae.


Assuntos
Vírus Gigantes , Camada de Gelo , Camada de Gelo/virologia , Groenlândia , Vírus Gigantes/genética , Vírus Gigantes/classificação , Vírus Gigantes/isolamento & purificação , Filogenia , Ecossistema , Genoma Viral , Metagenômica , Clorófitas/virologia , Clorófitas/genética , Metagenoma , Neve
7.
Mar Genomics ; 75: 101107, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38735672

RESUMO

Previously studies have reported that MAGs (Metagenome-assembled genomes) belong to "Candidatus Manganitrophaceae" of phylum Nitrospirota with chemolithoautotrophic manganese oxidation potential exist in freshwater and hydrothermal environments. However, Nitrospirota members with chemolithoautotrophic manganese oxidation potential have not been reported in other marine environments. Through metagenomic sequencing, assembly and binning, nine metagenome-assembled genomes belonging to Nitrospirota are recovered from sediment of different depths in the polymetallic nodule area. Through the key functional genes annotation results, we find that these Nitrospirota have limited potential to oxidize organic carbon because of incomplete tricarboxylic acid cycle and most of them (6/9) have carbon dioxide fixation potential through different pathway (rTCA, WL or CBB). One MAG belongs to order Nitrospirales has the potential to use manganese oxidation to obtain energy for carbon fixation. In addition to manganese ions, the oxidation of inorganic nitrogen, sulfur, hydrogen and carbon monoxide may also provide energy for the growth of these Nitrospirota. In addition, different metal ion transport systems can help those Nitrospirota to resist heavy metal in sediment. Our work expands the understanding of the metabolic potential of Nitrospirota in sediment of polymetallic nodule region and may contributes to promoting the study of chemolithoautotrophic manganese oxidation.


Assuntos
Genoma Bacteriano , Sedimentos Geológicos , Metagenoma , Sedimentos Geológicos/microbiologia , Oceano Pacífico , Manganês/metabolismo , Bactérias/genética , Bactérias/classificação
8.
Appl Microbiol Biotechnol ; 108(1): 329, 2024 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-38727750

RESUMO

Xylanases are key biocatalysts in the degradation of the ß-1,4-glycosidic linkages in the xylan backbone of hemicellulose. These enzymes are potentially applied in a wide range of bioprocessing industries under harsh conditions. Metagenomics has emerged as powerful tools for the bioprospection and discovery of interesting bioactive molecules from extreme ecosystems with unique features, such as high temperatures. In this study, an innovative combination of function-driven screening of a compost metagenomic library and automatic extraction of halo areas with in-house MATLAB functions resulted in the identification of a promising clone with xylanase activity (LP4). The LP4 clone proved to be an effective xylanase producer under submerged fermentation conditions. Sequence and phylogenetic analyses revealed that the xylanase, Xyl4, corresponded to an endo-1,4-ß-xylanase belonging to glycosyl hydrolase family 10 (GH10). When xyl4 was expressed in Escherichia coli BL21(DE3), the enzyme activity increased about 2-fold compared to the LP4 clone. To get insight on the interaction of the enzyme with the substrate and establish possible strategies to improve its activity, the structure of Xyl4 was predicted, refined, and docked with xylohexaose. Our data unveiled, for the first time, the relevance of the amino acids Glu133 and Glu238 for catalysis, and a close inspection of the catalytic site suggested that the replacement of Phe316 by a bulkier Trp may improve Xyl4 activity. Our current findings contribute to enhancing the catalytic performance of Xyl4 towards industrial applications. KEY POINTS: • A GH10 endo-1,4-ß-xylanase (Xyl4) was isolated from a compost metagenomic library • MATLAB's in-house functions were developed to identify the xylanase-producing clones • Computational analysis showed that Glu133 and Glu238 are crucial residues for catalysis.


Assuntos
Compostagem , Endo-1,4-beta-Xilanases , Escherichia coli , Metagenômica , Filogenia , Endo-1,4-beta-Xilanases/genética , Endo-1,4-beta-Xilanases/metabolismo , Endo-1,4-beta-Xilanases/química , Endo-1,4-beta-Xilanases/isolamento & purificação , Escherichia coli/genética , Escherichia coli/metabolismo , Metagenoma , Biblioteca Gênica , Microbiologia do Solo , Xilanos/metabolismo , Clonagem Molecular , Fermentação , Expressão Gênica , Simulação de Acoplamento Molecular
9.
Nat Commun ; 15(1): 3543, 2024 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-38730244

RESUMO

ß-N-Acetylgalactosamine-containing glycans play essential roles in several biological processes, including cell adhesion, signal transduction, and immune responses. ß-N-Acetylgalactosaminidases hydrolyze ß-N-acetylgalactosamine linkages of various glycoconjugates. However, their biological significance remains ambiguous, primarily because only one type of enzyme, exo-ß-N-acetylgalactosaminidases that specifically act on ß-N-acetylgalactosamine residues, has been documented to date. In this study, we identify four groups distributed among all three domains of life and characterize eight ß-N-acetylgalactosaminidases and ß-N-acetylhexosaminidase through sequence-based screening of deep-sea metagenomes and subsequent searching of public protein databases. Despite low sequence similarity, the crystal structures of these enzymes demonstrate that all enzymes share a prototype structure and have diversified their substrate specificities (oligosaccharide-releasing, oligosaccharide/monosaccharide-releasing, and monosaccharide-releasing) through the accumulation of mutations and insertional amino acid sequences. The diverse ß-N-acetylgalactosaminidases reported in this study could facilitate the comprehension of their structures and functions and present evolutionary pathways for expanding their substrate specificity.


Assuntos
Acetilgalactosamina , Glicosídeo Hidrolases , Metagenoma , Metagenoma/genética , Especificidade por Substrato , Acetilgalactosamina/metabolismo , Acetilgalactosamina/química , Glicosídeo Hidrolases/metabolismo , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/química , beta-N-Acetil-Hexosaminidases/metabolismo , beta-N-Acetil-Hexosaminidases/genética , beta-N-Acetil-Hexosaminidases/química , Filogenia , Cristalografia por Raios X , Sequência de Aminoácidos , Animais
10.
Int J Mol Sci ; 25(9)2024 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-38731876

RESUMO

This study explores the impact of defecation frequency on the gut microbiome structure by analyzing fecal samples from individuals categorized by defecation frequency: infrequent (1-3 times/week, n = 4), mid-frequent (4-6 times/week, n = 7), and frequent (daily, n = 9). Utilizing 16S rRNA gene-based sequencing and LC-MS/MS metabolome profiling, significant differences in microbial diversity and community structures among the groups were observed. The infrequent group showed higher microbial diversity, with community structures significantly varying with defecation frequency, a pattern consistent across all sampling time points. The Ruminococcus genus was predominant in the infrequent group, but decreased with more frequent defecation, while the Bacteroides genus was more common in the frequent group, decreasing as defecation frequency lessened. The infrequent group demonstrated enriched biosynthesis genes for aromatic amino acids and branched-chain amino acids (BCAAs), in contrast to the frequent group, which had a higher prevalence of genes for BCAA catabolism. Metabolome analysis revealed higher levels of metabolites derived from aromatic amino acids and BCAA metabolism in the infrequent group, and lower levels of BCAA-derived metabolites in the frequent group, consistent with their predicted metagenomic functions. These findings underscore the importance of considering stool consistency/frequency in understanding the factors influencing the gut microbiome.


Assuntos
Defecação , Fezes , Microbioma Gastrointestinal , RNA Ribossômico 16S , Microbioma Gastrointestinal/genética , Humanos , RNA Ribossômico 16S/genética , Fezes/microbiologia , Masculino , Adulto , Feminino , Metaboloma , Biodiversidade , Aminoácidos de Cadeia Ramificada/metabolismo , Metabolômica/métodos , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Bacteroides/genética , Metagenoma
11.
Sci Rep ; 14(1): 11608, 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38773163

RESUMO

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic substances. On soils contaminated with PAHs, crop cultivation, animal husbandry and even the survival of microflora in the soil are greatly perturbed, depending on the degree of contamination. Most microorganisms cannot tolerate PAH-contaminated soils, however, some microbial strains can adapt to these harsh conditions and survive on contaminated soils. Analysis of the metagenomes of contaminated environmental samples may lead to discovery of PAH-degrading enzymes suitable for green biotechnology methodologies ranging from biocatalysis to pollution control. In the present study, our goal was to apply a metagenomic data search to identify efficient novel enzymes in remediation of PAH-contaminated soils. The metagenomic hits were further analyzed using a set of bioinformatics tools to select protein sequences predicted to encode well-folded soluble enzymes. Three novel enzymes (two dioxygenases and one peroxidase) were cloned and used in soil remediation microcosms experiments. The experimental design of the present study aimed at evaluating the effectiveness of the novel enzymes on short-term PAH degradation in the soil microcosmos model. The novel enzymes were found to be efficient for degradation of naphthalene and phenanthrene. Adding the inorganic oxidant CaO2 further increased the degrading potential of the novel enzymes for anthracene and pyrene. We conclude that metagenome mining paired with bioinformatic predictions, structural modelling and functional assays constitutes a powerful approach towards novel enzymes for soil remediation.


Assuntos
Biodegradação Ambiental , Metagenômica , Hidrocarbonetos Policíclicos Aromáticos , Microbiologia do Solo , Poluentes do Solo , Metagenômica/métodos , Hidrocarbonetos Policíclicos Aromáticos/metabolismo , Poluentes do Solo/metabolismo , Solo/química , Dioxigenases/metabolismo , Dioxigenases/genética , Dioxigenases/química , Fenantrenos/metabolismo , Naftalenos/metabolismo , Metagenoma
12.
Sci Rep ; 14(1): 11634, 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38773202

RESUMO

Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225-146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses.


Assuntos
Metagenômica , Ácaros , Filogenia , Animais , Ácaros/genética , Ácaros/classificação , Metagenômica/métodos , Genoma Mitocondrial , Mitocôndrias/genética , Metagenoma , Evolução Molecular , Ecossistema
13.
Front Cell Infect Microbiol ; 14: 1384809, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38774631

RESUMO

Introduction: Sharing microbiome data among researchers fosters new innovations and reduces cost for research. Practically, this means that the (meta)data will have to be standardized, transparent and readily available for researchers. The microbiome data and associated metadata will then be described with regards to composition and origin, in order to maximize the possibilities for application in various contexts of research. Here, we propose a set of tools and protocols to develop a real-time FAIR (Findable. Accessible, Interoperable and Reusable) compliant database for the handling and storage of human microbiome and host-associated data. Methods: The conflicts arising from privacy laws with respect to metadata, possible human genome sequences in the metagenome shotgun data and FAIR implementations are discussed. Alternate pathways for achieving compliance in such conflicts are analyzed. Sample traceable and sensitive microbiome data, such as DNA sequences or geolocalized metadata are identified, and the role of the GDPR (General Data Protection Regulation) data regulations are considered. For the construction of the database, procedures have been realized to make data FAIR compliant, while preserving privacy of the participants providing the data. Results and discussion: An open-source development platform, Supabase, was used to implement the microbiome database. Researchers can deploy this real-time database to access, upload, download and interact with human microbiome data in a FAIR complaint manner. In addition, a large language model (LLM) powered by ChatGPT is developed and deployed to enable knowledge dissemination and non-expert usage of the database.


Assuntos
Microbiota , Humanos , Microbiota/genética , Bases de Dados Factuais , Metadados , Metagenoma , Disseminação de Informação , Biologia Computacional/métodos , Metagenômica/métodos , Bases de Dados Genéticas
14.
World J Microbiol Biotechnol ; 40(6): 193, 2024 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-38709343

RESUMO

The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.


Assuntos
Bactérias , Biodegradação Ambiental , Metais Pesados , Metais Pesados/metabolismo , Bactérias/genética , Bactérias/metabolismo , Bactérias/efeitos dos fármacos , Genoma Bacteriano , Proteômica , Transcriptoma , Metagenômica , Metagenoma , Genômica , Farmacorresistência Bacteriana/genética
15.
Appl Microbiol Biotechnol ; 108(1): 338, 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38771321

RESUMO

Fucosyl-oligosaccharides (FUS) provide many health benefits to breastfed infants, but they are almost completely absent from bovine milk, which is the basis of infant formula. Therefore, there is a growing interest in the development of enzymatic transfucosylation strategies for the production of FUS. In this work, the α-L-fucosidases Fuc2358 and Fuc5372, previously isolated from the intestinal bacterial metagenome of breastfed infants, were used to synthesize fucosyllactose (FL) by transfucosylation reactions using p-nitrophenyl-α-L-fucopyranoside (pNP-Fuc) as donor and lactose as acceptor. Fuc2358 efficiently synthesized the major fucosylated human milk oligosaccharide (HMO) 2'-fucosyllactose (2'FL) with a 35% yield. Fuc2358 also produced the non-HMO FL isomer 3'-fucosyllactose (3'FL) and traces of non-reducing 1-fucosyllactose (1FL). Fuc5372 showed a lower transfucosylation activity compared to Fuc2358, producing several FL isomers, including 2'FL, 3'FL, and 1FL, with a higher proportion of 3'FL. Site-directed mutagenesis using rational design was performed to increase FUS yields in both α-L-fucosidases, based on structural models and sequence identity analysis. Mutants Fuc2358-F184H, Fuc2358-K286R, and Fuc5372-R230K showed a significantly higher ratio between 2'FL yields and hydrolyzed pNP-Fuc than their respective wild-type enzymes after 4 h of transfucosylation. The results with the Fuc2358-F184W and Fuc5372-W151F mutants showed that the residues F184 of Fuc2358 and W151 of Fuc5372 could have an effect on transfucosylation regioselectivity. Interestingly, phenylalanine increases the selectivity for α-1,2 linkages and tryptophan for α-1,3 linkages. These results give insight into the functionality of the active site amino acids in the transfucosylation activity of the GH29 α-L-fucosidases Fuc2358 and Fuc5372. KEY POINTS: Two α-L-fucosidases from infant gut bacterial microbiomes can fucosylate glycans Transfucosylation efficacy improved by tailored point-mutations in the active site F184 of Fuc2358 and W151 of Fuc5372 seem to steer transglycosylation regioselectivity.


Assuntos
Microbioma Gastrointestinal , Metagenoma , Leite Humano , Trissacarídeos , alfa-L-Fucosidase , alfa-L-Fucosidase/genética , alfa-L-Fucosidase/metabolismo , Humanos , Trissacarídeos/metabolismo , Leite Humano/química , Lactose/metabolismo , Oligossacarídeos/metabolismo , Mutagênese Sítio-Dirigida , Lactente , Fucose/metabolismo
16.
Nat Commun ; 15(1): 4066, 2024 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-38744885

RESUMO

Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.


Assuntos
Archaea , Genoma Arqueal , Fontes Termais , Metagenoma , Metagenômica , Filogenia , Fontes Termais/microbiologia , Archaea/genética , Archaea/classificação , China , Metagenômica/métodos , Biodiversidade , Concentração de Íons de Hidrogênio , Enxofre/metabolismo , Temperatura , Ecossistema
17.
BMC Bioinformatics ; 25(1): 191, 2024 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-38750423

RESUMO

BACKGROUND: The application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and whole metagenome sequencing approaches but has not been widely adopted as a technique. A major barrier to adoption is the lack of read simulation software built to handle characteristic features of these novel approaches. Reduced metagenomic sequencing (RMS) produces unique patterns of fragmentation per genome that are sensitive to restriction enzyme choice, and the non-uniform size selection of these fragments may introduce novel challenges to taxonomic assignment as well as relative abundance estimates. RESULTS: Through the development and application of simulation software, readsynth, we compare simulated metagenomic sequencing libraries with existing RMS data to assess the influence of multiple library preparation and sequencing steps on downstream analytical results. Based on read depth per position, readsynth achieved 0.79 Pearson's correlation and 0.94 Spearman's correlation to these benchmarks. Application of a novel estimation approach, fixed length taxonomic ratios, improved quantification accuracy of simulated human gut microbial communities when compared to estimates of mean or median coverage. CONCLUSIONS: We investigate the possible strengths and weaknesses of applying the RMS technique to profiling microbial communities via simulations with readsynth. The choice of restriction enzymes and size selection steps in library prep are non-trivial decisions that bias downstream profiling and quantification. The simulations investigated in this study illustrate the possible limits of preparing metagenomic libraries with a reduced representation sequencing approach, but also allow for the development of strategies for producing and handling the sequence data produced by this promising application.


Assuntos
Metagenoma , Metagenômica , Software , Metagenoma/genética , Metagenômica/métodos , Humanos , Análise de Sequência de DNA/métodos , Microbioma Gastrointestinal/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos
18.
Aquat Toxicol ; 271: 106925, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38718521

RESUMO

Excessive antibiotic use has led to the spread of antibiotic resistance genes (ARGs), impacting gut microbiota and host health. However, the effects of antibiotics on amphibian populations remain unclear. We investigated the impact of oxytetracycline (OTC) and ciprofloxacin (CIP) on Chinese giant salamanders (Andrias davidianus), focusing on gut microbiota, ARGs, and gene expression by performing metagenome and transcriptome sequencing. A. davidianus were given OTC (20 or 40 mg/kg) or CIP (50 or 100 mg/kg) orally for 7 days. The results revealed that oral administration of OTC and CIP led to distinct changes in microbial composition and functional potential, with CIP treatment having a greater impact than OTC. Antibiotic treatment also influenced the abundance of ARGs, with an increase in fluoroquinolone and multi-drug resistance genes observed post-treatment. The construction of metagenome-assembled genomes (MAGs) accurately validated that CIP intervention enriched fish-associated potential pathogens Aeromonas hydrophila carrying an increased number of ARGs. Additionally, mobile genetic elements (MGEs), such as phages and plasmids, were implicated in the dissemination of ARGs. Transcriptomic analysis of the gut revealed significant alterations in gene expression, particularly in immune-related pathways, with differential effects observed between OTC and CIP treatments. Integration of metagenomic and transcriptomic data highlighted potential correlations between gut gene expression and microbial composition, suggesting complex interactions between the host gut and its gut microbiota in response to antibiotic exposure. These findings underscore the importance of understanding the impact of antibiotic intervention on the gut microbiome and host health in amphibians, particularly in the context of antibiotic resistance and immune function.


Assuntos
Antibacterianos , Ciprofloxacina , Microbioma Gastrointestinal , Oxitetraciclina , Urodelos , Animais , Oxitetraciclina/toxicidade , Microbioma Gastrointestinal/efeitos dos fármacos , Ciprofloxacina/farmacologia , Ciprofloxacina/toxicidade , Urodelos/genética , Urodelos/microbiologia , Antibacterianos/toxicidade , Antibacterianos/farmacologia , Transcriptoma/efeitos dos fármacos , Metagenoma , Metagenômica , Perfilação da Expressão Gênica , Poluentes Químicos da Água/toxicidade , Aeromonas hydrophila/efeitos dos fármacos , Regulação da Expressão Gênica/efeitos dos fármacos
19.
Fish Shellfish Immunol ; 149: 109617, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38723876

RESUMO

Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn Macrobrachiumrosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.


Assuntos
Microbioma Gastrointestinal , Palaemonidae , Animais , Palaemonidae/imunologia , Palaemonidae/virologia , Palaemonidae/microbiologia , Palaemonidae/genética , Metagenômica , Metagenoma , Iridoviridae/fisiologia
20.
Sci Rep ; 14(1): 10012, 2024 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-38693138

RESUMO

Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, ß-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a ß-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the ß-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the ß-glucosidase activity. However, Cu2+ and Mn2+ ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied ß-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.


Assuntos
Biomassa , Lagos , beta-Glucosidase , beta-Glucosidase/genética , beta-Glucosidase/metabolismo , beta-Glucosidase/química , Lagos/microbiologia , Metagenômica/métodos , Escherichia coli/genética , Escherichia coli/metabolismo , Metagenoma , Clonagem Molecular , Estabilidade Enzimática , Hidrólise , Concentração de Íons de Hidrogênio , Celulose/metabolismo , Temperatura , Glucose/metabolismo
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