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Journal of Cancer Research and... Aug 2023This study aimed to investigate the differences in the composition of microbial communities and related functions in hepatocellular carcinoma (HCC) tumours and matched...
AIMS
This study aimed to investigate the differences in the composition of microbial communities and related functions in hepatocellular carcinoma (HCC) tumours and matched normal tissues were investigated.
METHODS AND MATERIAL
Tumour tissues and matched normal samples were collected from 30 HCC patients. Genomic DNA was collected and subjected to sequencing of the V3 + V4 region of the 16S rRNA gene. The microbial community profiles and metabolic pathway predictions of the different groups were characterized and compared.
RESULTS
Tumour and adjacent tissues had similar microbiota compositions but differed in abundance. Proteobacteria and Firmicutes abundance decreased and Cyanobacteria and Acidobacteria abundance increased in the tumour tissue. The microbial community diversity was higher in the tumour tissues than in adjacent samples, with potentially more dominant taxa in the adjacent tissues, including Firmicutes, Proteobacteria, and Actinobacteria. Acidobacteria, Cyanobacteria, and Chloroflexi were the dominant microbes in tumour tissues. A total of 46 metabolic pathways were identified. Global and overview maps were the most abundant pathways, followed by carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport. The top 50 most highly correlated microbial genera included Klebsiella, Rhodococcus, Ochrobactrum, and Azoarcus. Fonticella, Haloimpatiens, Brevibacterium, and Acidothermus were positively correlated with other microbial genera. The microbiota of adjacent tissues was more robust in the network analysis.
CONCLUSIONS
This study revealed differences in microbial composition between HCC tumour tissues and normal tissues and differences in microbial abundance associated with different metabolic functions. Cyanobacteria, Proteobacteria, and Actinobacteria may play important roles in HCC.
Topics: Humans; Carcinoma, Hepatocellular; RNA, Ribosomal, 16S; Liver Neoplasms; Energy Metabolism
PubMed: 37675712
DOI: 10.4103/jcrt.jcrt_139_22 -
In Vivo (Athens, Greece) 2023High-fat diets induce shifts in the gut microbial community structure in patients or animals with non-alcoholic steatohepatitis (NASH). The objective of this study was...
BACKGROUND/AIM
High-fat diets induce shifts in the gut microbial community structure in patients or animals with non-alcoholic steatohepatitis (NASH). The objective of this study was to investigate the influence of metformin (MET) and berberine (BER) on the intestinal microbiota of rats with NASH.
MATERIALS AND METHODS
Forty specific pathogen-free male Sprague-Dawley rats were randomized into 4 groups. Model rats were fed high-fat diets to create NASH models. MET or BER rats were administrated MET or BER, respectively, at the onset of induction of NASH. Serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), cholesterol, and triglycerides were examined. Plasma endotoxin levels were measured using the turbidimetric endotoxin assay. The incidence of bacterial translocation describes the passage of bacteria of the gastrointestinal tract through the intestinal mucosa barrier to mesenteric lymph nodes and other organs. Hematoxylin and eosin and oil red O staining were used for histopathological analysis. High throughput 16S rRNA sequencing was carried out for analyzing the composition of intestinal microbiota.
RESULTS
High-fat diets caused NASH after 16-week induction. Administration of MET and BER ameliorated NASH by attenuating hepatic steatosis and inflammation and decreasing the plasma levels of endotoxin. MET and BER restored the composition of the intestinal microbiota disrupted by NASH. Both MET and BER altered the abundance of Atopobiaceae, Brevibacterium, Christensenellaceae, Coriobacteriales, Papillibacter, Pygmaiobacter, and Rikenellaceae RC9 in rats with NASH. The screened intestinal microbiota may be responsible for the improvement in fat accumulation and glucose metabolism.
CONCLUSION
MET and BER demonstrated beneficial effects on the intestinal microbiota, which was disturbed in NASH. This finding may explain the functional mechanism of MET and BER in NASH.
Topics: Humans; Rats; Male; Animals; Non-alcoholic Fatty Liver Disease; Berberine; Gastrointestinal Microbiome; Metformin; RNA, Ribosomal, 16S; Rats, Sprague-Dawley; Diet, High-Fat; Endotoxins; Liver; Disease Models, Animal
PubMed: 37652508
DOI: 10.21873/invivo.13308 -
Heliyon May 2024Investigating oat tissue microflora during its different developmental stages is necessary for understanding its growth and anti-disease mechanism. In this study, 16S...
Investigating oat tissue microflora during its different developmental stages is necessary for understanding its growth and anti-disease mechanism. In this study, 16S rDNA and ITS (Internally Transcribed Spacer) high-throughput sequencing technology were used to explore the microflora diversity of oat tissue. Twenty-seven samples of leaves, stems, and roots from three developmental stages, namely the seedling stage (SS), jointing stage (JS), and maturity stage (MS), underwent sequencing analysis. The analysis showed that 6480 operational taxonomic units (OTUs) were identified in the examined samples, of which 1698 were fungal and 4782 were bacterial. Furthermore, 126 OTUs were shared by fungi, mainly , , and at the phylum level, and 39 OTUs were shared by bacteria, mainly and at the phylum level. The microbial diversity of oat tissue in the three developmental stages showed differences, and the α-diversity of the bacteria and β-diversity of the bacteria and fungi in the roots were higher than those of the stems and leaves. Among the bacteria species, , and were predominant in the leaves, MND1 was predominant in the roots, and was predominant in the stems. Moreover, maintained a stable state at all growth stages. In the fungal species, was dominant in the leaves, was dominant in the roots, and was dominant in the stems. All species with a high abundance were related to the growth process of oats and antagonistic bacteria. Furthermore, connection modules were denser in bacterial than in fungal populations. The samples were treated with superoxide dismutase and peroxidase. There were 42 strains associated with SOD (Superoxide dismutase), 60 strains associated with POD (Peroxidase), and 38 strains in total, which much higher than fungi. The network analysis showed that bacteria might have more dense connection modules than fungi, The number of bacterial connections to enzymes were much higher than that of fungi. Furthermore, these results provide a basis for further mechanistic research.
PubMed: 38711667
DOI: 10.1016/j.heliyon.2024.e30276 -
Cells Nov 2023In bacteria, the Rho protein mediates Rho-dependent termination (RDT) by identifying a non-specific cytosine-rich Rho utilization site on the newly synthesized RNA. As a...
In bacteria, the Rho protein mediates Rho-dependent termination (RDT) by identifying a non-specific cytosine-rich Rho utilization site on the newly synthesized RNA. As a result of RDT, downstream RNA transcription is reduced. Due to the bias in reverse transcription and PCR amplification, we could not identify the RDT site by directly measuring the amount of mRNA upstream and downstream of RDT sites. To overcome this difficulty, we employed a 77 bp reporter gene , (coding tRNA) from , and we transcriptionally fused it to the sequences to be assayed. We constructed a series of plasmids by combining a segment of the galactose () operon sequences, both with and without the RDT regions at the ends of cistrons (, , and ) upstream of . The RNA polymerase will transcribe the operon sequence and unless it encounters the RDT encoded by the inserted sequence. Since the quantitative real-time PCR (qRT-PCR) method detects the steady state following mRNA synthesis and degradation, we observed that tRNA is degraded at the same rate in these transcriptional fusion plasmids. Therefore, the amount of tRNA can directly reflect the mRNA synthesis. Using this approach, we were able to effectively assay the RDTs and Rho-independent termination (RIT) in the operon by quantifying the relative amount of tRNA using qRT-PCR analyses. The resultant RDT% for , g, and at the end of were 36, 26, and 63, individually. The resultant RIT% at the end of the operon is 33%. Our findings demonstrate that combining tRNA with qRT-PCR can directly measure RIT, RDT, or any other signal that attenuates transcription efficiencies in vivo, making it a useful tool for gene expression research.
Topics: Base Sequence; Genes, Reporter; Real-Time Polymerase Chain Reaction; RNA, Transfer, Arg; RNA; RNA, Messenger
PubMed: 37998331
DOI: 10.3390/cells12222596 -
Antibiotics (Basel, Switzerland) Aug 2023This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in...
This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in colostrum and milk samples from cows. Three groups of healthy dairy cows ( = 24) with different antibiotic treatments during DCT were studied. Colostrum and milk samples from Month 0 (M0), 2 (M2), 4 (M4) and 6 (M6) were analysed using whole-genome shotgun-sequencing. The microbial diversity from antibiotic-treated groups was different and higher than that of the non-antibiotic group. This difference was more evident in milk compared to colostrum, with increasing diversity seen only in antibiotic-treated groups. The microbiome of antibiotic-treated groups clustered separately from the non-antibiotic group at M2-, M4- and M6 milk samples, showing the effect of antibiotic treatment on between-group (beta) diversity. The non-antibiotic group did not show a high relative abundance of mastitis-causing pathogens during early lactation and was more associated with genera such as , , and . A high relative abundance of antibiotic resistance genes (ARGs) was observed in the milk of antibiotic-treated groups with the Cephaguard group showing a significantly high abundance of genes conferring resistance to cephalosporin, aminoglycoside and penam classes. The data support the use of non-antibiotic alternatives for drying off in cows.
PubMed: 37627735
DOI: 10.3390/antibiotics12081315 -
The Journal of Antimicrobial... May 2024Corynebacterium (C.) sp. 22KM0430 related to C. oculi and isolated from a dog exhibited resistance to tetracycline, and its WGS analysis revealed a putative resistance...
BACKGROUND
Corynebacterium (C.) sp. 22KM0430 related to C. oculi and isolated from a dog exhibited resistance to tetracycline, and its WGS analysis revealed a putative resistance gene on a 35 562-bp plasmid also harbouring the MLSB resistance gene erm(X).
OBJECTIVES
To characterize the novel tetracycline resistance gene tet(65) and demonstrate its functionality by expression in C. glutamicum and Escherichia coli and plasmid curing of the host strain.
METHODS
tet(65) was cloned with and without its repressor tetR(65) and expressed in C. glutamicum DSM20300 and E. coli DH5α. Plasmid was cured by non-selective passages. Minimal inhibitory concentrations (MICs) of tetracyclines were determined according to CLSI guidelines. Association of tet(65) with efflux was shown by the addition of reserpine to MIC assays. Phylogenetic position and transmembrane structure of Tet(65) were analysed using MEGA11 and DeepTMHMM.
RESULTS
Tet(65) shows 73% amino acid identity with the closest related Tet(Z), contains 12 transmembrane domains and is structurally related to the Major Facilitator Superfamily. The tetracycline MICs decreased in the plasmid-cured strain and increased when tet(65) was expressed in C. glutamicum and in E. coli. The MICs of tetracycline decreased in the presence of reserpine indicating that tet(65) functions as an efflux pump. A GenBank search also identified tet(65) in C. diphtheriae and Brevibacterium (B.) casei and B. luteolum.
CONCLUSIONS
A novel tetracycline efflux gene tet(65) was identified in a C. oculi related species and was also present in the human pathogen C. diphtheriae and in Brevibacterium species indicating broader potential for dissemination.
Topics: Plasmids; Tetracycline Resistance; Microbial Sensitivity Tests; Anti-Bacterial Agents; Escherichia coli; Corynebacterium; Animals; Drug Resistance, Multiple, Bacterial; Phylogeny; Dogs; Tetracycline; Cloning, Molecular; Corynebacterium Infections; Dog Diseases
PubMed: 38497972
DOI: 10.1093/jac/dkae066 -
BMC Genomics Oct 2023Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from...
Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, had its genome sequenced to study the biosynthetic potential to produce novel natural products within the Brevibacterium genus. The genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. Evaluating the antibacterial activity of strain H-BE7, it exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7's genome.
Topics: Brevibacterium; Ecosystem; Genomics; Phylogeny; Anti-Bacterial Agents; Multigene Family; Phenazines
PubMed: 37858045
DOI: 10.1186/s12864-023-09694-7 -
Plant Direct Dec 2023Tobacco wildfire disease caused by pv. is one of the most destructive foliar bacterial diseases occurring worldwide. However, the effect of wildfire disease on cigar...
Tobacco wildfire disease caused by pv. is one of the most destructive foliar bacterial diseases occurring worldwide. However, the effect of wildfire disease on cigar tobacco leaves has not been clarified in detail. In this study, the differences in microbiota and chemical factors between wildfire disease-infected leaves and healthy leaves were characterized using high-throughput Illumina sequencing and a continuous-flow analytical system, respectively. The results demonstrated significant alterations in the structure of the phyllosphere microbial community in response to wildfire disease, and the infection of pv. led to a decrease in bacterial richness and diversity. Furthermore, the content of nicotine, protein, total nitrogen, and Cl in diseased leaves significantly increased by 47.86%, 17.46%, 20.08%, and 72.77% in comparison to healthy leaves, while the levels of total sugar and reducing sugar decreased by 59.59% and 70.0%, respectively. Notably, the wildfire disease had little effect on the content of starch and K. Redundancy analysis revealed that , , , and displayed positive correlations with nicotine, protein, total nitrogen, Cl and K contents, while , , , , , , , and displayed positive correlations with total sugar and reducing sugar contents. , , and were found to be enriched in diseased leaves, suggesting their potential role in disease suppression. Co-occurrence network analysis indicated that positive correlations were prevalent in microbial networks, and the bacterial network of healthy tobacco leaves exhibited greater complexity compared to diseased tobacco leaves. This study revealed the impact of wildfire disease on the microbial community and chemical compositions of tobacco leaves and provides new insights for the biological control of tobacco wildfire disease.
PubMed: 38099080
DOI: 10.1002/pld3.551 -
Poultry Science Dec 2023Efforts to achieve sustainable phosphorus (P) inputs in broiler farming which meet the physiological demand of animals include nutritional intervention strategies that...
Efforts to achieve sustainable phosphorus (P) inputs in broiler farming which meet the physiological demand of animals include nutritional intervention strategies that have the potential to modulate and utilize endogenous and microbiota-associated capacities. A temporal P conditioning strategy in broiler nutrition is promising as it induces endocrinal and transcriptional responses to maintain mineral homeostasis. In this context, the current study aims to evaluate the composition of the jejunal microbiota as a functional entity located at the main absorption site involved in nutrient metabolism. Starting from a medium or high P supply in the first weeks of life of broilers, a depletion strategy was applied at growth intervals from d 17 to 24 and d 25 to 37 to investigate the consequences on the composition of the jejunal microbiota. The results on fecal mineral P, calcium (Ca), and phytate contents showed that the diets applied to the depleted and non-depleted cohorts were effective. Microbial diversity in jejunum was represented by alpha diversity indices which appeared unaffected between dietary groups. However, chickens assigned to the dietary P depletion groups showed significantly higher abundances of Facklamia, Lachnospiraceae, and Ruminococcaceae compared to non-depleted control groups. Based on current knowledge of microbial function, these microorganisms make only a minor contribution to the birds' adaptive mechanism in the jejunum following P depletion. Microbial taxa such as Brevibacterium, Brachybacterium, and genera of the Staphylococcaceae family proliferated in a P-enriched environment and might be considered biomarkers for excessive P supply in commercial broiler chickens.
Topics: Animals; Phosphorus; Jejunum; Chickens; Minerals; Diet; Microbiota; Animal Feed; Dietary Supplements; Animal Nutritional Physiological Phenomena
PubMed: 37797492
DOI: 10.1016/j.psj.2023.103096 -
Microbiology Spectrum Aug 2023The microbiome profiles of poultry production systems significantly impact bird health, welfare, and the environment. This study investigated the influence of...
The microbiome profiles of poultry production systems significantly impact bird health, welfare, and the environment. This study investigated the influence of broiler-rearing systems on the microbiome composition of commercial and backyard chicken farms and their environment over time. Understanding these effects is vital for optimizing animal growth, enhancing welfare, and addressing human and environmental health implications. We collected and analyzed various samples from commercial and backyard farms, revealing significant differences in microbial diversity measurements between the two systems. Backyard farms exhibited higher alpha diversity measurements in soil and water samples, while commercial farms showed higher values for litter and feeder samples. The differences in microbial diversity were also reflected in the relative abundance of various microbial taxa. In backyard farms, Proteobacteria levels increased over time, while Firmicutes levels decreased. Campilobacterota, including the major poultry foodborne pathogen , increased over time in commercial farm environments. Furthermore, , associated with improved growth performance in chickens, were more abundant in backyard farms. Conversely, pathogenic was significantly higher in backyard chicken fecal and feeder swab samples. The presence of and , associated with low-performing broiler flocks, was significantly higher in commercial farm samples. The observed differences in microbial composition and diversity suggest that farm management practices and environmental conditions significantly affect poultry health and welfare and have potential implications for human and environmental health. Understanding these relationships can inform targeted interventions to optimize poultry production, improve animal welfare, and mitigate foodborne pathogens and antimicrobial resistance risks. IMPORTANCE The microbiome of poultry production systems has garnered significant attention due to its implications on bird health, welfare, and overall performance. The present study investigates the impact of different broiler-rearing systems, namely, commercial (conventional) and backyard (non-conventional), on the microbiome profiles of chickens and their environment over time. Understanding the influence of these systems on microbiome composition is a critical aspect of the One-Health concept, which emphasizes the interconnectedness of animal, human, and environmental health. Our findings demonstrate that the type of broiler production system significantly affects both the birds and their environment, with distinct microbial communities associated with each system. This study reveals the presence of specific microbial taxa that differ in abundance between commercial and backyard poultry farms, providing valuable insights into the management practices that may alter the microbiome in these settings. Furthermore, the dynamic changes in microbial composition over time observed in our study highlight the complex interplay between the poultry gut microbiome, environmental factors, and production systems. By identifying the key microbial players and their fluctuations in commercial and backyard broiler production systems, this research offers a foundation for developing targeted strategies to optimize bird health and welfare while minimizing the potential risks to human and environmental health. The results contribute to a growing body of knowledge in the field of poultry microbiome research and have the potential to guide future improvements in poultry production practices that promote a sustainable and healthy balance between the birds, their environment, and the microbial communities they host.
PubMed: 37607066
DOI: 10.1128/spectrum.01682-23