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Frontiers in Microbiology 2021Intestinal infections are a major cause of morbidity and mortality in humans and agricultural animals, especially newborns and weaned animals. Preventive treatments that...
Intestinal infections are a major cause of morbidity and mortality in humans and agricultural animals, especially newborns and weaned animals. Preventive treatments that help weaned animals maintain homeostasis and balance the hindgut microbial populations are desirable. The present study aimed to explore the impact of bacitracin methylene disalicylate (BMD) on the intestinal health by analyzing the intestinal environment, morphology, expression of peptidoglycan recognition proteins (PGRPs), and flora of weaned rabbits. A total of 300 New Zealand weaned rabbits were randomly divided into the following five treatment groups for a 35-day feed trial: control group (basal diet), bacitracin zinc (BZ) group (50 mg/kg BZ), BMDa group (100 mg/kg BMD), BMDb group (50 mg/kg BMD), and BMDc group (rabbits fed a basal diet supplemented with 25 mg/kg BMD). In each treatment group, 28 rabbits were slaughtered for experimental analysis. The results showed that the supplementation of BMD increased the environmental acidity of the cecum of the weaned rabbits and reduced the ammonia-nitrogen concentration, which was beneficial to the survival of useful bacteria in the intestine. The morphology analysis of the duodenum using hematoxylin and eosin staining revealed that the villus length, villus/crypt ratio, and intestinal wall thickness increased in the BMD group, thereby improving the structure of the duodenum and the absorption capacity of the small intestine. Moreover, real-time polymerase chain reaction test showed that PGRPs (especially PGLYRP-1 and PGLYRP-2) in the intestinal had an antagonistic effect with BMD in the process of inhibiting pathogenic bacteria, resulting in their decreased expression ( < 0.05). Furthermore, through 16S rRNA sequencing in the cecal content, the abundance of the predominant phyla in the BMDa and BZ groups was found to be the closest. The abundance of the genera , ), (), , (), , , and increased in the BMDa and BZ groups ( < 0.05). The relative abundance of , , and significantly increased only in the BMDa group ( < 0.05). Conclusively, BMD, as well as microbes, improved the intestinal environment and structure to maintain the intestinal health of weaned rabbits.
PubMed: 34248860
DOI: 10.3389/fmicb.2021.579006 -
Antibiotics (Basel, Switzerland) Jul 2022This study used 16S rRNA sequencing to evaluate the effects of dry cow antimicrobial therapy on the udder milk microbiota by comparing the microbial populations in milk...
This study used 16S rRNA sequencing to evaluate the effects of dry cow antimicrobial therapy on the udder milk microbiota by comparing the microbial populations in milk at dry-off (DRY) (~60 days before calving) and post-partum (FRESH) (4-11 days after calving) from cows receiving an intramammary antibiotic infusion prior to dry-off (IMT) and cows that did not receive treatment (CTL). Milk was collected from 23 cows from the IMT group and 27 cows from the CTL group. IMT and DRY samples had a greater correlation with the genera and , and the family Micrococcaceae, when compared to IMT and FRESH samples. CTL group samples collected at DRY had a greater correlation with the genera and when compared to FRESH samples; no bacterial taxa were observed to have a significant correlation with FRESH samples in the CTL group. DRY samples collected from the CTL group had a greater correlation with the genus when compared to IMT and CTL samples. For DRY samples collected from the IMT group, a greater correlation with the genus when compared to DRY and CTL samples, was observed. The lack of a correlation for FRESH samples between the CTL and IMT treatment groups indicated that intramammary antimicrobial dry cow therapy had no significant effect on the udder milk microbiota post-partum.
PubMed: 35884217
DOI: 10.3390/antibiotics11070963 -
Microorganisms Sep 2021Periodontal and Endodontic diseases are biofilm-related diseases. The presence of microorganisms in root canals (RCs) and the complex microbiota of periodontal pockets...
Periodontal and Endodontic diseases are biofilm-related diseases. The presence of microorganisms in root canals (RCs) and the complex microbiota of periodontal pockets (PPs) contribute to the development of endodontic-periodontal diseases. This study performed a systemic analysis using state-of-the-art sequence data to assess the microbial composition of infected RCs and PPs to further assess the microbiota and verify the possibility of cross-infection between these sites. The microbiomes of these combined diseases were examined with a focus on the V3-V4 hypervariable region of the 16S rRNA gene. The number of species in PP was higher than in RC, and there was a predominance of obligate anaerobes and gram-negative bacteria. In the RCs, the genera , , predominated, in contrast, the PPs revealed a predominance of , , , and The RC and PP microbiome was not similar with regards to the sharing of OTUs for phyla and genera (8 and 67, respectively). The evaluation of molecular markers revealed a large number of markers for resistance to antibiotics of the carbapenem and beta-lactam type (broad spectrum). Another relevant finding of this study was the markers related to systemic diseases related to cardiac muscle and rheumatology, among others. In conclusion, the RC microbiota was less complex and diverse than PP. Interactions between microbial communities were present. The shared genus can signal communication between the endodontic and periodontal microbiomes.
PubMed: 34576820
DOI: 10.3390/microorganisms9091925 -
Heliyon May 2024The respiratory tract harbors a variety of microbiota, whose composition and abundance depend on specific site factors, interaction with external factors, and disease....
BACKGROUND
The respiratory tract harbors a variety of microbiota, whose composition and abundance depend on specific site factors, interaction with external factors, and disease. The aim of this study was to investigate the relationship between COVID-19 severity and the nasopharyngeal microbiome.
METHODS
We conducted a prospective cohort study in Mexico City, collecting nasopharyngeal swabs from 30 COVID-19 patients and 14 healthy volunteers. Microbiome profiling was performed using 16S rRNA gene analysis. Taxonomic assignment, classification, diversity analysis, core microbiome analysis, and statistical analysis were conducted using R packages.
RESULTS
The microbiome data analysis revealed taxonomic shifts within the nasopharyngeal microbiome in severe COVID-19. Particularly, we observed a significant reduction in the relative abundance of and genera in critically ill COVID-19 patients (p < 0.001). In contrast, these patients exhibited a marked enrichment of , and genera (p < 0.01). Analysis of the core microbiome across all samples consistently identified the presence of , , and .
CONCLUSIONS
Our study suggests that the disruption of physicochemical conditions and barriers resulting from inflammatory processes and the intubation procedure in critically ill COVID-19 patients may facilitate the colonization and invasion of the nasopharynx by oral microorganisms.
PubMed: 38826746
DOI: 10.1016/j.heliyon.2024.e31562 -
Journal of Dairy Science Apr 2020Dairy cattle are globally important agricultural animals. Central to their biology is the rumen, which houses an essential microbial community, or microbiome, important...
Dairy cattle are globally important agricultural animals. Central to their biology is the rumen, which houses an essential microbial community, or microbiome, important for providing nutrition from otherwise host-inaccessible dietary components. The rumen environment is noted for its substantial spatial heterogeneity, as illustrated by the stratification into ruminal solid and liquid phases. A third microbiota found directly attached to the ruminal epithelium (the epimural microbiota) also exists but is less well understood because of challenges in sampling the ruminal epithelium. As a result, our understanding of the epimural microbiota is based on analyses of cannulated animals sampled at a single location-the ventral sac-and does not account for other ruminal locations, which may have importance for overall rumen function. To address this knowledge gap, we hypothesize that the epimural microbiota at different ruminal locations differs due to known morphological, physiological, and functional differences across the geographic spread of the rumen epithelium. Here, we characterized bacterial epimural communities at different sites within 8 lactating Holstein dairy cows using 16S rRNA gene sequencing. Four different sites were sampled via rumen tissue biopsy: cranial sac (CS), ventral sac (VS), caudodorsal blind sac (CDBS), and caudoventral blind sac (CVBS). We found that locations differed in both epimural bacterial community structure and composition, with the CDBS community displaying the greatest diversity. Across all sampling sites, epimural bacterial communities were dominated by members of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. Bacteria within Prevotellaceae, Butyrivibrio, Campylobacter, Mogibacterium, and Desulfobulbus all showed high relative sequence abundance and differential distributions according to sample location. There appears to be a core epimural microbiota present across all locations in all cows, although relative abundance was highly variable. The difference in relative abundance in epimural microbial communities, perhaps influenced by host physiology and the diversity within rumen contents, likely has important consequences for nutrition acquisition and general health. To the best of our knowledge, this work represents the first characterization of the ruminal epimural microbiota across different epithelial locations for any bovine ruminant.
Topics: Animals; Bacteria; Biodiversity; Cattle; Diet; Female; Lactation; Microbiota; RNA, Ribosomal, 16S; Rumen
PubMed: 32057427
DOI: 10.3168/jds.2019-17649 -
Frontiers in Veterinary Science 2017Colonic contents and mucosal scrapings from pigs inoculated with or were collected at necropsy and classified as either positive ( = 29) or negative ( = 7) for...
Colonic contents and mucosal scrapings from pigs inoculated with or were collected at necropsy and classified as either positive ( = 29) or negative ( = 7) for swine dysentery (SD) based upon lesions and positive culture from the source pig. The microbiota in each sample was analyzed by bacterial census taking (16S rRNA gene sequencing). Procrustes analysis revealed similar clustering by disease classification with a relatively high M2 value (0.44) suggesting differences in the microbiota between mucosal and luminal samples from the same pig. In both sample types, differences in richness and beta diversity were observed between disease statuses ( ≤ 0.014). The relative abundance of , and was higher in pigs with dysentery for both mucosal scrapings and luminal samples while , and were significantly more abundant in the luminal contents only. For inoculated pigs that did not develop dysentery, were more abundant in both sample types, and were more abundant in mucosal scrapings, and and were more abundant in luminal contents when compared with diseased pigs. Linear discriminant analysis of effect size revealed , and multiple spp. as differential features in mucosal scrapings from pigs with dysentery while and a spp. were differential in pigs without disease. These differential features were not observed in luminal samples. In summary, microbial profiles in both sample types differ significantly between disease states; however, evaluation of the mucosal microbiome specifically may be of higher value in elucidating bacterial mechanisms underlying development of SD.
PubMed: 28971100
DOI: 10.3389/fvets.2017.00139 -
Frontiers in Microbiology 2022Taxifolin (TAX), as a natural flavonoid, has been widely focused on due to its strong anti-oxidation, anti-inflammation, anti-virus, and even anti-tumor activity....
Taxifolin (TAX), as a natural flavonoid, has been widely focused on due to its strong anti-oxidation, anti-inflammation, anti-virus, and even anti-tumor activity. However, the effect of TAX on semen quality was unknown. The purpose of this study was to analyze the beneficial influences of adding feed additive TAX to boar semen in terms of its quality and potential mechanisms. We discovered that TAX increased sperm motility significantly in Duroc boars by the elevation of the protein levels such as ZAG, PKA, CatSper, and p-ERK for sperm quality. TAX increased the blood concentration of testosterone derivatives, antioxidants such as melatonin and betaine, unsaturated fatty acids such as DHA, and beneficial amino acids such as proline. Conversely, TAX decreased 10 different kinds of bile acids in the plasma. Moreover, TAX increased "beneficial" microbes such as , , and at the Genus level. However, TAX reduced the "harmful" intestinal bacteria such as , , and . There was a very close correlation between fecal microbes, plasma metabolites, and semen parameters by the spearman correlation analysis. Therefore, the data suggest that TAX increases the semen quality of Duroc boars by benefiting the gut microbes and blood metabolites. It is supposed that TAX could be used as a kind of feed additive to increase the semen quality of boars to enhance production performance.
PubMed: 36312933
DOI: 10.3389/fmicb.2022.1020628 -
Journal of Immunology (Baltimore, Md. :... Mar 2018Commensal bacteria are critical for physiological functions in the gut, and dysbiosis in the gut may cause diseases. In this article, we report that mice deficient in...
Commensal bacteria are critical for physiological functions in the gut, and dysbiosis in the gut may cause diseases. In this article, we report that mice deficient in cathelin-related antimicrobial peptide (CRAMP) were defective in the development of colon mucosa and highly sensitive to dextran sulfate sodium (DSS)-elicited colitis, as well as azoxymethane-mediated carcinogenesis. Pretreatment of CRAMP mice with antibiotics markedly reduced the severity of DSS-induced colitis, suggesting CRAMP as a limiting factor on dysbiosis in the colon. This was supported by observations that wild-type (WT) mice cohoused with CRAMP mice became highly sensitive to DSS-induced colitis, and the composition of fecal microbiota was skewed by CRAMP deficiency. In particular, several bacterial species that are typically found in oral microbiota, such as , , and , were increased in feces of CRAMP mice and were transferred to WT mice during cohousing. When littermates of CRAMP parents were examined, the composition of the fecal microbiota of WT pups and heterozygous parents was similar. In contrast, although the difference in fecal microbiota between CRAMP and WT pups was small early on after weaning and single mouse housing, there was an increasing divergence with prolonged single housing. These results indicate that CRAMP is critical in maintaining colon microbiota balance and supports mucosal homeostasis, anti-inflammatory responses, and protection from carcinogenesis.
Topics: Animals; Antimicrobial Cationic Peptides; Colitis; Colon; Disease Models, Animal; Feces; Gastrointestinal Microbiome; Homeostasis; Intestinal Mucosa; Mice; Mice, Inbred C57BL; Microbiota; Proteins; Cathelicidins
PubMed: 29440355
DOI: 10.4049/jimmunol.1602073 -
PloS One 2013Tuberculosis (TB) remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent...
BACKGROUND
Tuberculosis (TB) remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease.
METHODOLOGY/PRINCIPAL FINDINGS
Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. Proteobacteria and Bacteroidetes were more represented in the TB samples and Firmicutes was more predominant in the controls. Sixteen major bacterial genera were recovered. Streptococcus, Neisseria and Prevotella were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. Actinomyces, Fusobacterium, Leptotrichia, Prevotella, Streptococcus, and Veillonella were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera Mogibacterium, Moryella and Oribacterium were enriched statistically in the TB samples, while a genus belonging to the unclassified Lactobacillales was enriched in the controls. The diversity of microbiota was similar in the TB and control samples.
CONCLUSIONS/SIGNIFICANCE
The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.
Topics: Adult; Aged; Aged, 80 and over; Bacteria; Biodiversity; Case-Control Studies; Female; High-Throughput Nucleotide Sequencing; Humans; Male; Metagenome; Middle Aged; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sputum; Tuberculosis, Pulmonary
PubMed: 23365674
DOI: 10.1371/journal.pone.0054574 -
Scientific Reports Oct 2018Enrichment of calf diets with exogenous butyrate has shown promise as a promotor of calf growth and intestinal development. However, the impact of dietary derived...
Enrichment of calf diets with exogenous butyrate has shown promise as a promotor of calf growth and intestinal development. However, the impact of dietary derived butyrate on the gut microbiota and their potential role, in turn, as mediators of its effect on calf growth and development is not known. Here, the effects of butyrate supplementation on rumen and hindgut microbiota and fermentation profiles were assessed in 16 Holstein-Friesian bull calves randomly assigned to one of two groups: Control (CON) fed conventional milk replacer or Sodium-Butyrate (SB - added to milk replacer) from days 7 to 56 of life. In the colon, total short chain fatty acid (SCFA), propionate and acetate concentrations were increased by SB (P < 0.05). 16S rRNA gene amplicon sequencing showed cecal abundance of butyrate producers Butyrivibrio and Shuttleworthia were decreased by SB (P < 0.05), while that of the propionate producer Phascolarctobacterium was higher (P < 0.05). Mogibacterium is associated with impaired gut health and was reduced in the cecum of SB calves (P < 0.05). These data show that the beneficial effects of SB on growth and performance occur in tandem with changes in the abundance of important SCFA producing and health-associated bacteria in the hindgut in milk-fed calves.
Topics: Animals; Bacteria; Biodiversity; Butyrates; Cattle; Dairying; Fermentation; Food, Fortified; Gastrointestinal Microbiome; Gastrointestinal Tract; Male; Milk; Phylogeny; Principal Component Analysis; Rumen; Weaning
PubMed: 30297834
DOI: 10.1038/s41598-018-33122-6