RESUMO
The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since then, important features of their cell biology, physiology, ecology, and diversity have been revealed. Over the course of some 40 years, the diversity of known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most of this archaeal diversity has been revealed by environmental 16S rRNA gene amplicon sequencing surveys using a broad range of universal and targeted primers. Of the few primers that target a large fraction of known archaeal diversity, all display a bias against recently discovered lineages, which limits studies aiming to survey overall archaeal diversity. Induced by genomic exploration of archaeal diversity, and improved phylogenomics approaches, archaeal taxonomic classification has been frequently revised. Due to computational limitations and continued discovery of new lineages, a stable archaeal phylogeny is not yet within reach. Obtaining phylogenetic and taxonomic consensus of archaea should be a high priority for the archaeal research community.
Assuntos
Archaea , Ecologia , Archaea/genética , Genômica , Filogenia , RNA Ribossômico 16S/genéticaRESUMO
The intestinal barrier consists of mucosal, epithelial, and immunological barriers and serves as a dynamic interface between the host and its environment. Disruption of the intestinal barrier integrity is a leading cause of various gastrointestinal diseases, such as inflammatory bowel disease. The homeostasis of the intestinal barrier is tightly regulated by crosstalk between gut microbes and the immune system; however, the implication of the immune system on the imbalance of gut microbes that disrupts barrier integrity remains to be fully elucidated. An inhibitory immunoglobulin-like receptor, Allergin-1, is expressed on mast cells and dendritic cells and inhibits Toll-like receptor (TLR)-2 and TLR-4 signaling in these cells. Since TLRs are major sensors of microbiota and are involved in local epithelial homeostasis, we investigated the role of Allergin-1 in maintaining intestinal homeostasis. Allergin-1-deficient (Milr1-/-) mice exhibited more severe dextran sulfate sodium (DSS)-induced colitis than did wild-type (WT) mice. Milr1-/- mice showed an enhanced intestinal permeability compared with WT mice even before DSS administration. Treatment of Milr1-/- mice with neomycin, but not ampicillin, restored intestinal barrier integrity. The 16S rRNA gene sequencing analysis demonstrated that Bifidobacterium pseudolongum was the dominant bacterium in Milr1-/- mice after treatment with ampicillin. Although the transfer of B. pseudolongum to germ-free WT mice had no effect on intestinal permeability, its transfer into ampicillin-treated WT mice enhanced intestinal permeability. These results demonstrated that Allergin-1 deficiency enhanced intestinal dysbiosis with expanded B. pseudolongum, which contributes to intestinal barrier dysfunction in collaboration with neomycin-sensitive and ampicillin-resistant microbiota.
Assuntos
Disbiose , Mucosa Intestinal , Camundongos Endogâmicos C57BL , Camundongos Knockout , Animais , Disbiose/imunologia , Camundongos , Mucosa Intestinal/imunologia , Mucosa Intestinal/microbiologia , Mucosa Intestinal/metabolismo , Sulfato de Dextrana , Microbioma Gastrointestinal/imunologia , Colite/imunologia , Colite/microbiologia , Receptores Imunológicos/metabolismo , Receptores Imunológicos/genética , Receptores Imunológicos/imunologia , Neomicina/farmacologia , PermeabilidadeRESUMO
BACKGROUND: The selection of primer pairs in sequencing-based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We therefore propose PrimerEvalPy, a Python-based package designed to test the performance of any primer or primer pair against any sequencing database. The package calculates a coverage metric and returns the amplicon sequences found, along with information such as their average start and end positions. It also allows the analysis of coverage for different taxonomic levels. RESULTS: As a case study, PrimerEvalPy was used to test the most commonly used primers in the literature against two oral 16S rRNA gene databases containing bacteria and archaea. The results showed that the most commonly used primer pairs in the oral cavity did not match those with the highest coverage. The best performing primer pairs were found for the detection of oral bacteria and archaea. CONCLUSIONS: This demonstrates the importance of a coverage analysis tool such as PrimerEvalPy to find the best primer pairs for specific niches. The software is available under the MIT licence at https://gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy .
Assuntos
Archaea , Bactérias , Primers do DNA , Microbiota , RNA Ribossômico 16S , Software , Microbiota/genética , RNA Ribossômico 16S/genética , Bactérias/genética , Bactérias/classificação , Archaea/genética , Primers do DNA/metabolismo , Primers do DNA/genética , Humanos , Boca/microbiologia , Simulação por ComputadorRESUMO
BACKGROUND: Sequencing variable regions of the 16S rRNA gene (≃300 bp) with Illumina technology is commonly used to study the composition of human microbiota. Unfortunately, short reads are unable to differentiate between highly similar species. Considering that species from the same genus can be associated with health or disease it is important to identify them at the lowest possible taxonomic rank. Third-generation sequencing platforms such as PacBio SMRT, increase read lengths allowing to sequence the whole gene with the maximum taxonomic resolution. Despite its potential, full length 16S rRNA gene sequencing is not widely used yet. The aim of the current study was to compare the sequencing output and taxonomic annotation performance of the two approaches (Illumina short read sequencing and PacBio long read sequencing of 16S rRNA gene) in different human microbiome samples. DNA from saliva, oral biofilms (subgingival plaque) and faeces of 9 volunteers was isolated. Regions V3-V4 and V1-V9 were amplified and sequenced by Illumina Miseq and by PacBio Sequel II sequencers, respectively. RESULTS: With both platforms, a similar percentage of reads was assigned to the genus level (94.79% and 95.06% respectively) but with PacBio a higher proportion of reads were further assigned to the species level (55.23% vs 74.14%). Regarding overall bacterial composition, samples clustered by niche and not by sequencing platform. In addition, all genera with > 0.1% abundance were detected in both platforms for all types of samples. Although some genera such as Streptococcus tended to be observed at higher frequency in PacBio than in Illumina (20.14% vs 14.12% in saliva, 10.63% vs 6.59% in subgingival plaque biofilm samples) none of the differences were statistically significant when correcting for multiple testing. CONCLUSIONS: The results presented in the current manuscript suggest that samples sequenced using Illumina and PacBio are mostly comparable. Considering that PacBio reads were assigned at the species level with higher accuracy than Illumina, our data support the use of PacBio technology for future microbiome studies, although a higher cost is currently required to obtain an equivalent number of reads per sample.
Assuntos
Microbiota , Humanos , RNA Ribossômico 16S/genética , Genes de RNAr , Filogenia , Análise de Sequência de DNA/métodos , Microbiota/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodosRESUMO
Bacterial flora are present in various parts of the human body, including the intestine, and are thought to be involved in the etiology of various diseases such as multiple sclerosis, intestinal diseases, cancer, and uterine diseases. In recent years, the presence of bacterial 16S rRNA genes has been revealed in blood, which was previously thought to be a sterile environment, and characteristic blood microbiomes have been detected in various diseases. However, the mechanism and the origin of the bacterial information are unknown. In this study, we performed 16S rRNA metagenomic analysis of bacterial DNA in serum extracellular vesicles from five healthy donors and seven patients with renal cell carcinoma and detected Cutibacterium acnes DNA as a characteristic bacterial DNA in the serum extracellular vesicles of patients with renal cell carcinoma. In addition, C. acnes DNA was significantly reduced in postoperative serum extracellular vesicles from patients with renal cell carcinoma compared with that in preoperative serum extracellular vesicles from these patients and was also detected in tumor tissue and extracellular vesicles from tumor tissue-associated microbiota, suggesting an association between C. acnes extracellular vesicles and renal cell carcinoma. C. acnes extracellular vesicles were taken up by renal carcinoma cells to enhance their proliferative potential. C. acnes extracellular vesicles also exhibited tumor-promoting activity in a mouse model of renal cancer allografts with enhanced angiogenesis. These results suggest that extracellular vesicles released by C. acnes localized in renal cell carcinoma tissues act in a tumor-promoting manner.
Assuntos
Carcinoma de Células Renais , Vesículas Extracelulares , Neoplasias Renais , Vesículas Extracelulares/metabolismo , Carcinoma de Células Renais/microbiologia , Carcinoma de Células Renais/patologia , Humanos , Animais , Neoplasias Renais/microbiologia , Neoplasias Renais/patologia , Camundongos , RNA Ribossômico 16S/genética , Linhagem Celular Tumoral , Feminino , Proliferação de Células , DNA Bacteriano/genética , Propionibacteriaceae/genética , MasculinoRESUMO
Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90â% archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99â% of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.
Assuntos
Archaea , Bactérias , Microbiota , Filogenia , Poríferos , Poríferos/microbiologia , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Animais , Oceano Atlântico , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Água do Mar/microbiologia , RNA Ribossômico 16S/genética , BiodiversidadeRESUMO
BACKGROUND: The specific microbiota and associated metabolites linked to non-alcoholic fatty liver disease (NAFLD) are still controversial. Thus, we aimed to understand how the core gut microbiota and metabolites impact NAFLD. METHODS: The data for the discovery cohort were collected from the Guangzhou Nutrition and Health Study (GNHS) follow-up conducted between 2014 and 2018. We collected 272 metadata points from 1546 individuals. The metadata were input into four interpretable machine learning models to identify important gut microbiota associated with NAFLD. These models were subsequently applied to two validation cohorts [the internal validation cohort (n = 377), and the prospective validation cohort (n = 749)] to assess generalizability. We constructed an individual microbiome risk score (MRS) based on the identified gut microbiota and conducted animal faecal microbiome transplantation experiment using faecal samples from individuals with different levels of MRS to determine the relationship between MRS and NAFLD. Additionally, we conducted targeted metabolomic sequencing of faecal samples to analyse potential metabolites. RESULTS: Among the four machine learning models used, the lightGBM algorithm achieved the best performance. A total of 12 taxa-related features of the microbiota were selected by the lightGBM algorithm and further used to calculate the MRS. Increased MRS was positively associated with the presence of NAFLD, with odds ratio (OR) of 1.86 (1.72, 2.02) per 1-unit increase in MRS. An elevated abundance of the faecal microbiota (f__veillonellaceae) was associated with increased NAFLD risk, whereas f__rikenellaceae, f__barnesiellaceae, and s__adolescentis were associated with a decreased presence of NAFLD. Higher levels of specific gut microbiota-derived metabolites of bile acids (taurocholic acid) might be positively associated with both a higher MRS and NAFLD risk. FMT in mice further confirmed a causal association between a higher MRS and the development of NAFLD. CONCLUSIONS: We confirmed that an alteration in the composition of the core gut microbiota might be biologically relevant to NAFLD development. Our work demonstrated the role of the microbiota in the development of NAFLD.
Assuntos
Microbioma Gastrointestinal , Microbiota , Hepatopatia Gordurosa não Alcoólica , Pessoa de Meia-Idade , Humanos , Animais , Camundongos , Idoso , Hepatopatia Gordurosa não Alcoólica/epidemiologia , Hepatopatia Gordurosa não Alcoólica/metabolismo , Fígado/metabolismo , Vida IndependenteRESUMO
Broad-range 16S rRNA PCR and sequencing of 1,183 blood specimens from 853 unique patients yielded an interpretable sequence and bacterial identification in 29%, 16S rRNA amplification with uninterpretable sequences in 53%, and no amplification in 18%. This study highlights the potential utility of this technique in identifying fastidious gram-negative and anaerobic bacteria but the frequent recovery of environmental and contaminant organisms argues for its judicious use. IMPORTANCE: The existing literature focuses on its performance compared to blood cultures in patients with sepsis, leaving a gap in the literature regarding other blood specimens in suspected infectious syndrome across the severity spectrum. We aimed to characterize its microbiological outcomes and provide insight into its potential clinical utility.
Assuntos
RNA Ribossômico 16S , Humanos , RNA Ribossômico 16S/genética , Estudos Retrospectivos , DNA Bacteriano/genética , Reação em Cadeia da Polimerase/métodos , Canadá , Análise de Sequência de DNARESUMO
Streams impacted by historic mining activity are characterized by acidic pH, unique microbial communities, and abundant metal-oxide precipitation, all of which can influence groundwater-surface water exchange. We investigate how metal-oxide precipitates and hyporheic mixing mediate the composition of microbial communities in two streams receiving acid-rock and mine drainage near Silverton, Colorado, USA. A large, neutral pH hyporheic zone facilitated the precipitation of metal particles/colloids in hyporheic porewaters. A small, low pH hyporheic zone, limited by the presence of a low-permeability, iron-oxyhydroxide layer known as ferricrete, led to the formation of steep geochemical gradients and high dissolved-metal concentrations. To determine how these two hyporheic systems influence microbiome composition, we installed well clusters and deployed in situ microcosms in each stream to sample porewaters and sediments for 16S rRNA gene sequencing. Results indicated that distinct hydrogeochemical conditions were present above and below the ferricrete in the low pH system. A positive feedback loop may be present in the low pH stream where microbially mediated precipitation of iron-oxides contributes to additional clogging of hyporheic pore spaces, separating abundant, iron-oxidizing bacteria (Gallionella spp.) above the ferricrete from rare, low-abundance bacteria below the ferricrete. Metal precipitates and colloids that formed in the neutral pH hyporheic zone were associated with a more diverse phylogenetic community of nonmotile, nutrient-cycling bacteria that may be transported through hyporheic pore spaces. In summary, biogeochemical conditions influence, and are influenced by, hyporheic mixing, which mediates the distribution of micro-organisms and, thus, the cycling of metals in streams receiving acid-rock and mine drainage. IMPORTANCE: In streams receiving acid-rock and mine drainage, the abundant precipitation of iron minerals can alter how groundwater and surface water mix along streams (in what is known as the "hyporheic zone") and may shape the distribution of microbial communities. The findings presented here suggest that neutral pH streams with large, well-mixed hyporheic zones may harbor and transport diverse microorganisms attached to particles/colloids through hyporheic pore spaces. In acidic streams where metal oxides clog pore spaces and limit hyporheic exchange, iron-oxidizing bacteria may dominate and phylogenetic diversity becomes low. The abundance of iron-oxidizing bacteria in acid mine drainage streams has the potential to contribute to additional clogging of hyporheic pore spaces and the accumulation of toxic metals in the hyporheic zone. This research highlights the dynamic interplay between hydrology, geochemistry, and microbiology at the groundwater-surface water interface of acid mine drainage streams.
Assuntos
Ferro , Microbiota , Filogenia , RNA Ribossômico 16S/genética , Óxidos , Metais , Bactérias/genética , Água/química , ColoidesRESUMO
BACKGROUND: Although stag beetles are a popular saprophytic insect, their gut microbiome has been poorly studied. Here, 16 S rRNA gene sequencing was employed to reveal the gut microbiota composition and functional variations between wild and domestic Dorcus hopei hopei (Dhh) larval individuals. RESULTS: The results indicated a significant difference between the wild and domestic Dhh gut microbiota., the domestic Dhh individuals contained more gut microbial taxa (e.g. genera Ralstonia and Methyloversatilis) with xenobiotic degrading functions. The wild Dhh possesses gut microbiota compositions (e.g. Turicibacter and Tyzzerella ) more appropriate for energy metabolism and potential growth. This study furthermore assigned all Dhh individuals by size into groups for data analysis; which indicated limited disparities between the gut microbiota of different-sized D. hopei hopei larvae. CONCLUSION: The outcome of this study illustrated that there exists a significant discrepancy in gut microbiota composition between wild and domestic Dhh larvae. In addition, the assemblage of gut microbiome in Dhh was primarily attributed to environmental influences instead of individual differences such as developmental potential or size. These findings will provide a valuable theoretical foundation for the protection of wild saprophytic insects and the potential utilization of the insect-associated intestinal microbiome in the future.
Assuntos
Besouros , Microbioma Gastrointestinal , Animais , Besouros/genética , Microbioma Gastrointestinal/genética , Larva , RNA Ribossômico 16S/genéticaRESUMO
BACKGROUND: Extrauterine growth restriction (EUGR) represents a prevalent condition observed in preterm neonates, which poses potential adverse implications for both neonatal development and long-term health outcomes. The manifestation of EUGR has been intricately associated with perturbations in microbial and metabolic profiles. This study aimed to investigate the characteristics of the gut microbial network in early colonizers among preterm neonates with EUGR. METHODS: Twenty-nine preterm infants participated in this study, comprising 14 subjects in the EUGR group and 15 in the normal growth (AGA) group. Meconium (D1) and fecal samples were collected at postnatal day 28 (D28) and 1 month after discharge (M1). Subsequently, total bacterial DNA was extracted and sequenced using the Illumina MiSeq system, targeting the V3-V4 hyper-variable regions of the 16S rRNA gene. RESULTS: The outcomes of principal coordinates analysis (PCoA) and examination of the microbial network structure revealed distinctive developmental trajectories in the gut microbiome during the initial three months of life among preterm neonates with and without EUGR. Significant differences in microbial community were observed at the D1 (P = 0.039) and M1 phases (P = 0.036) between the EUGR and AGA groups, while a comparable microbial community was noted at the D28 phase (P = 0.414). Moreover, relative to the AGA group, the EUGR group exhibited significantly lower relative abundances of bacteria associated with secretion of short-chain fatty acids, including Lactobacillus (P = 0.041) and Parabacteroides (P = 0.033) at the D1 phase, Bifidobacterium at the D28 phase, and genera Dysgonomonas (P = 0.042), Dialister (P = 0.02), Dorea (P = 0.042), and Fusobacterium (P = 0.017) at the M1 phase. CONCLUSION: Overall, the present findings offer crucial important insights into the distinctive gut microbial signatures exhibited by earlier colonizers in preterm neonates with EUGR. Further mechanistic studies are needed to establish whether these differences are the cause or a consequence of EUGR.
Assuntos
Microbioma Gastrointestinal , Recém-Nascido Prematuro , Lactente , Recém-Nascido , Humanos , Idade Gestacional , RNA Ribossômico 16S/genética , Peso ao NascerRESUMO
BACKGROUND: Accurate identification of bacterial communities is crucial for research applications, diagnostics, and clinical interventions. Although 16S ribosomal RNA (rRNA) gene sequencing is a widely employed technique for bacterial taxonomic classification, it often results in misclassified or unclassified bacterial taxa. This study sought to refine the full-length 16S rRNA gene sequencing protocol using the MinION sequencer, focusing on the V1-V9 regions. Our methodological enquiry examined several factors, including the number of PCR amplification cycles, choice of primers and Taq polymerase, and specific sequence databases and workflows employed. We used a microbial standard comprising eight bacterial strains (five gram-positive and three gram-negative) in known proportions as a validation control. RESULTS: Based on the MinION protocol, we employed the microbial standard as the DNA template for the 16S rRNA gene amplicon sequencing procedure. Our analysis showed that an elevated number of PCR amplification cycles introduced PCR bias, and the selection of Taq polymerase and primer sets significantly affected the subsequent analysis. Bacterial identification at genus level demonstrated Pearson correlation coefficients ranging from 0.73 to 0.79 when assessed using BugSeq, Kraken-Silva and EPI2ME-16S workflows. Notably, the EPI2ME-16S workflow exhibited the highest Pearson correlation with the microbial standard, minimised misclassification, and increased alignment accuracy. At the species taxonomic level, the BugSeq workflow was superior, with a Pearson correlation coefficient of 0.92. CONCLUSIONS: These findings emphasise the importance of careful selection of PCR settings and a well-structured analytical framework for 16S rRNA full-length gene sequencing. The results showed a robust correlation between the predicted and observed bacterial abundances at both the genus and species taxonomic levels, making these findings applicable across diverse research contexts and with clinical utility for reliable pathogen identification.
Assuntos
Nanoporos , RNA Ribossômico 16S/genética , Taq Polimerase/genética , Genes de RNAr , Análise de Sequência de DNA/métodos , DNA Bacteriano/genética , Bactérias/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodosRESUMO
Persistent human papillomavirus (HPV) infection can lead to cervical intraepithelial neoplasia (CIN) and cervical cancer, posing serious threats to the health of women. Although the cervicovaginal microbiota is strongly associated with CIN, the dynamics of the microbiota during CIN development are unknown. In this retrospective cohort study, we analyzed 3-year longitudinal data from 72 patients diagnosed with a persistent HPV infection almost all caused by high-risk HPV types. Patients were categorized into groups with HPV persistent infection (n = 37), progression to CIN (n = 16), and CIN regression (n = 19) based on infection outcome during the follow-up period. Furthermore, 16S rRNA gene sequencing was performed on consecutively collected cervical samples to explore the composition and dynamics of the cervicovaginal microbiota during the development and regression of CIN. Our results showed that the composition of the cervicovaginal microbiota varied among women with different HPV infection outcomes and remained relatively stable during the follow-up period. Notably, the serial follow-up data showed that these microbial alterations were present for at least 1-2 years and occurred before pathologic changes. In addition, microbial markers that were highly discriminatory for CIN progression or regression were identified. This study provides evidence for a temporal relationship between changes in the cervicovaginal microbiota and the development of CIN, and our findings provide support for future microbial intervention strategies for CIN.
Assuntos
Microbiota , Infecções por Papillomavirus , Displasia do Colo do Útero , Neoplasias do Colo do Útero , Humanos , Feminino , RNA Ribossômico 16S/genética , Estudos Retrospectivos , Colo do Útero , Microbiota/genética , Papillomaviridae/genéticaRESUMO
Methamphetamine (MA) is a highly addictive mental stimulant, and MA abuse remains a significant public health problem worldwide, while effective treatment options are limited. Lycium barbarum polysaccharide (LBP), a major effective component extracted from Lycium barbarum, has potential health-promoting effects on the nervous system; however, its role in MA dependence remains unclear. In this study, the conditioned place preference (CPP) of MA addiction in adult male mice was established to detect changes in gut microbiota profiles after LBP treatment through 16S rRNA gene sequencing. Our results found that LBP administration could alleviate MA-induced CPP and hyperactivity. Interestingly, LBP improved MA-induced gut microbiota dysbiosis by increasing some beneficial autochthonous genus abundances, such as Allobaculum, Gordonibacter, and Ileibacterium. MA exposure induced the co-occurrence network of intestinal microbiota to become weaker and more unstable when compared with the control group, while LBP changed the above effects when compared with the MA group. Bacterial gene function prediction showed that amphetamine addiction, cocaine addiction, and short-chain fatty acid metabolism were enriched. These findings reveal that LBP might regulate MA-induced gut microbiota and behavior changes, which showed potential therapeutic applicability in treating MA addiction by regulating the gut microbiota.
Assuntos
Transtornos Relacionados ao Uso de Anfetaminas , Medicamentos de Ervas Chinesas , Disbiose , Microbioma Gastrointestinal , Metanfetamina , Animais , Microbioma Gastrointestinal/efeitos dos fármacos , Metanfetamina/farmacologia , Disbiose/induzido quimicamente , Disbiose/microbiologia , Masculino , Camundongos , Medicamentos de Ervas Chinesas/farmacologia , Medicamentos de Ervas Chinesas/administração & dosagem , RNA Ribossômico 16S/análise , Camundongos Endogâmicos C57BL , Bactérias/efeitos dos fármacos , Bactérias/classificação , Bactérias/isolamento & purificação , Bactérias/genéticaRESUMO
In the field of metagenomic research, the choice of DNA extraction methods plays a pivotal yet often underestimated role in shaping the reliability and interpretability of microbial community data. This study delves into the impact of five commercially available DNA extraction kits on the analysis of bovine fecal microbiota. Recognizing the importance of accurate DNA extraction in elucidating microbial community dynamics, we systematically assessed DNA yield, quality, and microbial composition across these kits using 16S rRNA gene sequencing. Notably, the FastDNA spin soil kit yielded the highest DNA concentration, while significant variations in quality were observed across kits. Furthermore, differential abundance analysis revealed kit-specific biases that impacted taxa representation. Microbial richness and diversity were significantly influenced by the choice of extraction kit, with QIAamp DNA stool minikit, QIAamp Power Pro, and DNeasy PowerSoil outperforming the Stool DNA Kit. Principal-coordinate analysis revealed distinct clustering based on DNA isolation procedures, particularly highlighting the unique microbial community composition derived from the Stool DNA Kit. This study also addressed practical implications, demonstrating how kit selection influences the concentration of Gram-positive and Gram-negative bacterial taxa in samples. This research highlights the need for consideration of DNA extraction kits in metagenomic studies, offering valuable insights for researchers striving to advance the precision and depth of microbiota analyses in ruminants.
Assuntos
DNA Bacteriano , Fezes , RNA Ribossômico 16S , Animais , Bovinos , Fezes/microbiologia , RNA Ribossômico 16S/genética , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/classificação , Metagenômica , Análise de Sequência de DNA , Kit de Reagentes para Diagnóstico/normas , Microbiota/genéticaRESUMO
A strictly anaerobic, motile bacterium, designated as strain Ai-910T, was isolated from the sludge of an anaerobic digestion tank in China. Cells were Gram-stain-negative rods. Optimal growth was observed at 38 °C (growth range 25-42 °C), pH 8.5 (growth range 5.5-10.5), and under a NaCl concentration of 0.06% (w/v) (range 0-2.0%). Major cellular fatty acids were iso-C15â:â0 and anteiso-C15â:â0. The respiratory quinone was MK-7. Using xylose as the growth substrate, succinate was produced as the fermentation product. Phylogenetic analysis based on the 16 S rRNA gene sequences indicated that strain Ai-910T formed a distinct phylogenetic lineage that reflects a new genus in the family Marinilabiliaceae, sharing high similarities to Alkaliflexus imshenetskii Z-7010T (92.78%), Alkalitalea saponilacus SC/BZ-SP2T (92.51%), and Geofilum rubicundum JAM-BA0501T (92.36%). Genomic similarity (average nucleotide identity and digital DNA-DNA hybridization) values between strain Ai-910T and its phylogenetic neighbors were below 65.27 and 16.90%, respectively, indicating that strain Ai-910T represented a novel species. The average amino acid identity between strain Ai-910T and other related members of the family Marinilabiliaceae were below 69.41%, supporting that strain Ai-910T was a member of a new genus within the family Marinilabiliaceae. Phylogenetic, genomic, and phenotypic analysis revealed that strain Ai-910T was distinguished from other phylogenetic relatives within the family Marinilabiliaceae. The genome size was 3.10 Mbp, and the DNA G + C content of the isolate was 42.8 mol%. Collectively, differences of the phenotypic and phylogenetic features of strain Ai-910T from its close relatives suggest that strain Ai-910T represented a novel species in a new genus of the family Marinilabiliaceae, for which the name Xiashengella succiniciproducens gen. nov., sp. nov. was proposed. The type strain of Xiashengella succiniciproducens is Ai-910T (= CGMCC 1.17893T = KCTC 25,304T).
Assuntos
Bactérias , Ácido Succínico , Anaerobiose , Filogenia , Succinatos , DNARESUMO
A Gram-negative, facultative anaerobic, non-motile and rod-shaped bacterium, designated 10c7w1T, was isolated from a human gastrointestinal tract. Colonies on agar plates were small, circular, smooth and beige. The optimal growth conditions were determined to be 37â°C, pH 7.0-7.5 and 0â% (w/v) NaCl. Comparative analysis of complete 16S rRNA gene sequences revealed that strain 10c7w1T showed the highest sequence similarity of 95.8â% to Ottowia beijingensis MCCC 1A01410T, followed by Ottowia thiooxydans (95.2â%) JCM 11629T. The average amino acid identity values between 10c7w1T and O. beijingensis MCCC 1A01410T and O. thiooxydans JCM 11629T were above 60â% (71.4 and 69.5â%). The average nucleotide identity values between strain 10c7w1T and O. beijingensis MCCC 1A01410T and O. thiooxydans JCM 11629T were 76.9 and 72.5â%, respectively. The dominant fatty acids (≥10â%) were straight chain ones, with summed feature 3 (C16â:â1 ω7c/C16â:â1 ω6c), summed feature 8 (C18â:â1 ω7c/C18â:â1 ω6c) and C16â:â00 being the most abundant. Q-8 was the only respiratory quinone. The major polar lipids of strain 10c7w1T were phosphatidylethanolamine, diphosphatidylglycerol and unknown lipids. The DNA G+C content of strain 10c7w1T was 63.6âmol%. On the basis of phylogenetic, phenotypic and chemotaxonomic data, strain 10c7w1T is considered to represent a novel species within the genus Ottowia, for which the name Ottowia cancrivicina sp. nov. is proposed. The type strain is 10c7w1T (=MCCC 1H01399T=KCTC 92200T).
Assuntos
Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , Estômago , RNA Ribossômico 16S/genética , Ácidos Graxos/química , Humanos , DNA Bacteriano/genética , Estômago/microbiologia , Hibridização de Ácido Nucleico , Ubiquinona , Fosfolipídeos/químicaRESUMO
A Gram-stain-positive, rod-shaped, non-spore-forming and non-motile bacterium, designated strain WY-16T. Growth was observed at 20-42 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7) and salinity of 0-3â% (w/v; optimum, 1â%). Phylogenetic analysis based on genome sequences indicated that WY-16T was affiliated to the family Microbacteriaceae and most closely related to Salinibacterium xinjiangense and Salinibacterium amurskyense. The average nucleotide identity values between strain WY-16T and S. xinjiangense and S. amurskyense were 74.7 and 72.5â%, respectively. The digital DNA-DNA hybridization values between strain WY-16T and S. xinjiangense and S. amurskyense were 19.6 and 18.6â%, respectively. The predominant fatty acids were anteiso-C15â:â0, iso-C16â:â0 and iso-C16â:â0 10-methyl. The major menaquinones were MK-12, MK-13, MK-14 and MK-15. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified glycolipid and one unidentified phospholipid. The cell-wall peptidoglycan contained 2,4-diaminobutyric acid as the diamino acid and ribose, rhamnose, glucose and galactose were the major cell-wall sugars. Based on phenotypic, genotypic and phylogenetic evidence, strain WY-16T represents a novel species in the genus Salinibacterium, for which the name Salinibacterium soli sp. nov. is proposed. The type strain is WY-16T (=GDMCC 1.4011T=JCM 36421T).
Assuntos
Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Lagos , Hibridização de Ácido Nucleico , Fosfolipídeos , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , Microbiologia do Solo , Vitamina K 2 , Ácidos Graxos/química , Ácidos Graxos/análise , RNA Ribossômico 16S/genética , Vitamina K 2/análogos & derivados , Vitamina K 2/análise , DNA Bacteriano/genética , Fosfolipídeos/química , Fosfolipídeos/análise , Lagos/microbiologia , Peptidoglicano , ChinaRESUMO
A novel ligninase-producing and cellulose-degrading actinobacterium, designated strain NEAU-A12T, was isolated from a soil sample collected from Aohan banner, Chifeng City, Inner Mongolia Autonomous Region, PR China. A polyphasic taxonomic study was used to establish the status of strain NEAU-A12T. 16S rRNA gene sequence analysis revealed that strain NEAU-A12T belonged to the genus Actinoplanes and showed the highest similarity (98.3â%) to Actinoplanes palleronii DSM 43940T, while showing less than 98.3â% similarity to other members of the genus Actinoplanes. The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and glycosylphosphatidylinositol. The diagnostic sugars in cell hydrolysates were determined to be arabinose, glucose and xylose. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H2). The major fatty acids were C15â:â0, C16â:â0, C16â:â1 ω7c and C17â:â0. Meanwhile, genomic analysis revealed a genome size of 10â192â524 bp and a DNA G+C content of 70.6âmol%, and indicated that strain NEAU-A12T had the potential to degrade lignin and cellulose, as well as produce bioactive compounds. In addition, the average nucleotide identity values between strain NEAU-A12T and its reference strains A. palleronii DSM 43940T, Actinoplanes regularis DSM 43151T, Actinoplanes philippinensis DSM 43019T, Actinoplanes xinjiangensis DSM 45184T and Actinoplanes italicus DSM 43146T were 80.3, 80.3, 84.1, 84.3 and 84.0â%, respectively. The levels of digital DNA-DNA hybridization between them were found to be 23.6â% (21.3-26.1â%), 23.8â% (21.5-26.3â%), 28.3â% (25.9-30.8â%), 28.6â% (26.0-30.9â%) and 28.4â% (26.2-31.1â%), respectively. Based on phenotypic, chemotaxonomic and genotypic data, strain NEAU-A12T is considered to represent a novel species of the genus Actinoplanes, for which the name Actinoplanes sandaracinus sp. nov. is proposed, with NEAU-A12T (=CCTCC AA 2020039T=DSM 112043T) as the type strain.
Assuntos
Actinoplanes , Celulose , Solo , RNA Ribossômico 16S/genética , Composição de Bases , Ácidos Graxos/química , Filogenia , Análise de Sequência de DNA , DNA Bacteriano/genética , Técnicas de Tipagem BacterianaRESUMO
A novel actinobacterium, strain ZYX-F-186T, was isolated from marine sediment sampled on Yongxing Island, Hainan Province, PR China. Based on the results of 16S rRNA gene sequence analysis, strain ZYX-F-186T belongs to the genus Phytohabitans, with high similarity to Phytohabitans kaempferiae KK1-3T (98.3â%), Phytohabitans rumicis K11-0047T (98.1â%), Phytohabitans flavus K09-0627T (98.1â%), Phytohabitans houttuyneae K11-0057T (97.9â%), Phytohabitans suffuscus K07-0523T (97.7â%), and Phytohabitans aurantiacus RD004123T (97.7â%). Phylogenetic analysis of 16S rRNA gene sequences showed that the strain formed a single subclade in the genus Phytohabitans. The novel isolate contained meso-diaminopimelic acid, d-glutamic acid, glycine, d-alanine, and l-lysine in the cell wall. The whole-cell sugars were xylose, arabinose, ribose, and rhamnose. The predominant menaquinones were MK-9(H8), MK-9(H6), and MK-9(H4). The characteristic phospholipids were phosphatidylethanolamine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylglycerol, and an unknown phospholipid. The major fatty acids (>5â%) were iso-C16â:â0, anteiso-C17â:â0, and iso-C18â:â0. Genome sequencing showed a DNA G+C content of 71.9âmol%. Low average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values demonstrated that strain ZYX-F-186T could be readily distinguished from its closely related species. Based on its phylogenetic, chemotaxonomic, and physiological characteristics, strain ZYX-F-186T represents a novel species of the genus Phytohabitans, for which the name Phytohabitans maris sp. nov. is proposed. The type strain is ZYX-F-186T (=CGMCC 4.8025T=CCTCC AA 2023025T=JCM 36507T).