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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 -
International Journal of Molecular... Nov 2022Little is known whether a combination Ile and added Val improves the growth of pigs offered very low protein (VLP) diets through changes in nutrients digestibility and...
Little is known whether a combination Ile and added Val improves the growth of pigs offered very low protein (VLP) diets through changes in nutrients digestibility and gut microbiota. The objective of this study was to investigate the effect of a mixture of Val above and Ile at NRC levels on growth, nutrient digestibility and gut microbiota in pigs fed with VLP diets. Forty, weaned piglets were assigned to: positive control: normal-protein-diet; negative control (NC): VLP diet supplemented with first four limiting amino acids; VA: NC with Val above NRC; IL: NC with Ile at NRC level; VAIL: NC with Val above and Ile at NRC levels. While both VAIL and VA groups completely recovered the inhibitory effects of VLP diets on feed intake, only VAIL partially recovered the negative effects of VLP diets on growth performance. VAIL and VA increased the thermal radiation and decreased the digestibility of nitrogen. NC increased the relative abundance of and in the colon. VAIL had a higher abundance of colonic , and and the colon content of VA was more enriched with . Overall, VAIL partially improved the growth performance which is likely linked with alterations in gut microbiota composition.
Topics: Swine; Animals; Isoleucine; Diet, Protein-Restricted; Animal Feed; Valine; Diet; Dietary Supplements; Animal Nutritional Physiological Phenomena; Digestion
PubMed: 36499225
DOI: 10.3390/ijms232314886 -
PloS One 2014The function of the appendix is largely unknown, but its microbiota likely contributes to function. Alterations in microbiota may contribute to appendicitis, but...
PURPOSE
The function of the appendix is largely unknown, but its microbiota likely contributes to function. Alterations in microbiota may contribute to appendicitis, but conventional culture studies have not yielded conclusive information. We conducted a pilot, culture-independent 16S rRNA-based microbiota study of paired appendix and rectal samples.
METHODS
We collected appendix and rectal swabs from 21 children undergoing appendectomy, six with normal appendices and fifteen with appendicitis (nine perforated). After DNA extraction, we amplified and sequenced 16S rRNA genes and analyzed sequences using CLoVR. We identified organisms differing in relative abundance using ANOVA (p<0.05) by location (appendix vs. rectum), disease (appendicitis vs. normal), and disease severity (perforated vs. non-perforated).
RESULTS
We identified 290 taxa in the study's samples. Three taxa were significantly increased in normal appendices vs. normal rectal samples: Fusibacter (p = 0.009), Selenomonas (p = 0.026), and Peptostreptococcus (p = 0.049). Five taxa were increased in abundance in normal vs. diseased appendices: Paenibacillaceae (p = 0.005), Acidobacteriaceae GP4 (p = 0.019), Pseudonocardinae (p = 0.019), Bergeyella (p = 0.019) and Rhizobium (p = 0.045). Twelve taxa were increased in the appendices of appendicitis patients vs. normal appendix: Peptostreptococcus (p = 0.0003), Bilophila (p = 0.0004), Bulleidia (p = 0.012), Fusobacterium (p = 0.018), Parvimonas (p = 0.003), Mogibacterium (p = 0.012), Aminobacterium (p = 0.019), Proteus (p = 0.028), Actinomycineae (p = 0.028), Anaerovorax (p = 0.041), Anaerofilum (p = 0.045), Porphyromonas (p = 0.010). Five taxa were increased in appendices in patients with perforated vs. nonperforated appendicitis: Bulleidia (p = 0.004), Fusibacter (p = 0.005), Prevotella (p = 0.021), Porphyromonas (p = 0.030), Dialister (p = 0.035). Three taxa were increased in rectum samples of patients with appendicitis compared to the normal patients: Bulleidia (p = 0.034), Dialister (p = 0.003), and Porphyromonas (p = 0.026).
CONCLUSION
Specific taxa are more abundant in normal appendices compared to the rectum, suggesting that a distinctive appendix microbiota exists. Taxa with altered abundance in diseased and severely diseased (perforated) samples may contribute to appendicitis pathogenesis, and may provide microbial signatures in the rectum useful for guiding both treatment and diagnosis of appendicitis.
Topics: Adolescent; Appendectomy; Appendicitis; Appendix; Child; Child, Preschool; Female; Fusobacterium; Humans; Infant; Infant, Newborn; Male; Porphyromonas; RNA, Ribosomal, 16S; Rectum; Rhizobium
PubMed: 24759879
DOI: 10.1371/journal.pone.0095414 -
Animal : An International Journal of... Jun 2023Cattle represent a high contribution of the livestock's greenhouse gas emissions, mainly in the form of methane. Essential oils are a group of plant secondary...
Cattle represent a high contribution of the livestock's greenhouse gas emissions, mainly in the form of methane. Essential oils are a group of plant secondary metabolites obtained from volatile fractions of plants that have been shown to exert changes in the rumen fermentation and may alter feed efficiency and to reduce methane production. The objective of this study was to investigate the effect on rumen microbial population, CH emissions and milking performance of a mixture of essential oils (Agolin Ruminant, Switzerland) incorporated daily in the ration of dairy cattle. Forty Holstein cows (644 ± 63.5 kg of BW producing 41.2 ± 6.44 kg/d of milk with 190 ± 28.3 DIM) were divided into two treatments (n = 20) for 13 wk and housed in a single pen equipped with electronic feeding gates to control access to feed and monitor individual DM intake (DMI) on a daily basis. Treatments consisted of no supplementation (Control) or supplementation of 1 g/d of a blend of essential oils (BEOs) fed in the TMR. Individual milk production was recorded using electronic milk meters on a daily basis. Methane emissions were recorded using sniffers at the exit of the milking parlour. At day 64 of the study, a sample of rumen fluid was collected from 12 cows per treatment after the morning feeding using a stomach tube. There were no differences in DMI, milk yield, or milk composition between the two treatments. However, cows on BEO exhaled less CH (444 ± 12.5 l/d) than cows on Control (479 ± 12.5 l/d), and exhaled less (P < 0.05) CH/kg of DM consumed (17.6 vs 20.1 ± 0.53 l/kg, respectively) from the first week of study, with no interaction with time, which suggests a fast action of BEO of CH emissions. Rumen relative abundance of Entodonium increased, and those of Fusobacteria, Chytridiomycota, Epidinium, and Mogibacterium decreased in BEO compared with Control cows. Supplementing 1 g/d of BEO reduces CH emissions on absolute terms (l/d) and diminishes the amount of CH produced by unit of DM consumed by cows relatively soon after the first supplementation, and the effect is sustained over time without impacting intake or milking performance.
Topics: Female; Cattle; Animals; Milk; Diet; Lactation; Oils, Volatile; Methane; Rumen; Dietary Supplements; Microbiota; Fermentation; Silage
PubMed: 37196578
DOI: 10.1016/j.animal.2023.100825 -
PloS One 2012Recent reports have suggested the involvement of gut microbiota in the progression of colorectal cancer (CRC). We utilized pyrosequencing based analysis of 16S rRNA...
Recent reports have suggested the involvement of gut microbiota in the progression of colorectal cancer (CRC). We utilized pyrosequencing based analysis of 16S rRNA genes to determine the overall structure of microbiota in patients with colorectal cancer and healthy controls; we investigated microbiota of the intestinal lumen, the cancerous tissue and matched noncancerous normal tissue. Moreover, we investigated the mucosa-adherent microbial composition using rectal swab samples because the structure of the tissue-adherent bacterial community is potentially altered following bowel cleansing. Our findings indicated that the microbial structure of the intestinal lumen and cancerous tissue differed significantly. Phylotypes that enhance energy harvest from diets or perform metabolic exchange with the host were more abundant in the lumen. There were more abundant Firmicutes and less abundant Bacteroidetes and Proteobacteria in lumen. The overall microbial structures of cancerous tissue and noncancerous tissue were similar; however the tumor microbiota exhibited lower diversity. The structures of the intestinal lumen microbiota and mucosa-adherent microbiota were different in CRC patients compared to matched microbiota in healthy individuals. Lactobacillales was enriched in cancerous tissue, whereas Faecalibacterium was reduced. In the mucosa-adherent microbiota, Bifidobacterium, Faecalibacterium, and Blautia were reduced in CRC patients, whereas Fusobacterium, Porphyromonas, Peptostreptococcus, and Mogibacterium were enriched. In the lumen, predominant phylotypes related to metabolic disorders or metabolic exchange with the host, Erysipelotrichaceae, Prevotellaceae, and Coriobacteriaceae were increased in cancer patients. Coupled with previous reports, these results suggest that the intestinal microbiota is associated with CRC risk and that intestinal lumen microflora potentially influence CRC risk via cometabolism or metabolic exchange with the host. However, mucosa-associated microbiota potentially affects CRC risk primarily through direct interaction with the host.
Topics: Base Sequence; Case-Control Studies; Colorectal Neoplasms; DNA Primers; Humans; Intestinal Mucosa; Intestines; Polymerase Chain Reaction
PubMed: 22761885
DOI: 10.1371/journal.pone.0039743 -
Endocrine Connections Jul 2019The pathogenesis of Graves' disease (GD) remains unclear. In terms of environmental factors, GD development may be associated with chronic inflammation caused by...
OBJECTIVES
The pathogenesis of Graves' disease (GD) remains unclear. In terms of environmental factors, GD development may be associated with chronic inflammation caused by alteration of the intestinal flora. This study explored the association of intestinal flora alteration with the development of GD among the Han population in southwest China.
DESIGN AND METHODS
Fifteen GD patients at the Affiliated Hospital of Zunyi Medical College between March 2016 and March 2017 were randomly enrolled. Additionally, 15 sex- and age-matched healthy volunteers were selected as the control group during the same period. Fresh stool samples were collected, and bacterial 16S RNA was extracted and amplified for gene sequencing with the Illumina MiSeq platform. The sequencing results were subjected to operational taxonomic unit-based classification, classification verification, alpha diversity analysis, taxonomic composition analysis and partial least squares-discriminant analysis (PLS-DA).
RESULTS
The diversity indices for the GD group were lower than those for the control group. The GD group showed significantly higher abundances of Firmicutes, Proteobacteria and Actinobacillus and a higher Firmicutes/Bacteroidetes ratio than the control group. PLS-DA suggested the satisfactory classification of the flora between the GD group and the control group. The abundances of the genera Oribacterium, Mogibacterium, Lactobacillus, Aggregatibacter and Mogibacterium were significantly higher in the GD group than in the control group (P < 0.05).
CONCLUSIONS
The intestinal flora of GD patients was significantly different from that of the healthy population. Thus, alteration of intestinal flora may be associated with the development of GD.
PubMed: 31137015
DOI: 10.1530/EC-19-0001 -
Asian-Australasian Journal of Animal... Sep 2017The effect of flavonoids from alfalfa on the microbial flora was determined using molecular techniques of 16S ribosome deoxyribonucleic acid (rDNA) analysis.
OBJECTIVE
The effect of flavonoids from alfalfa on the microbial flora was determined using molecular techniques of 16S ribosome deoxyribonucleic acid (rDNA) analysis.
METHODS
Four primiparous Holstein heifers fitted with ruminal cannulas were used in a 4×4 Latin square design and fed a total mixed ration to which alfalfa flavonoids extract (AFE) was added at the rates of 0 (A, control), 20 (B), 60 (C), or 100 (D) mg per kg of heifer BW.
RESULTS
The number of operational taxonomic units in heifers given higher levels of flavonoid extract (C and D) was higher than for the two other treatments. The Shannon, Ace, and Chao indices for treatment C were significantly higher than for the other treatments (p<0.05). The number of phyla and genera increased linearly with increasing dietary supplementation of AFE (p<0.05). The principal co-ordinates analysis plot showed substantial differences in the microbial flora for the four treatments. The microbial flora in treatment A was similar to that in B, C, and D were similar by the weighted analysis. The richness of at the phylum level tended to increase with increasing AFE (p = 0.10). The proportion of at the phylum level increased linearly, whereas the proportion of decreased linearly with increasing AFE supplementation (p = 0.04). The percentage of , , and at the genus level decreased linearly with increasing AFE (p<0.05). The abundance of , , and at the genus level tended to decrease linearly with increasing AFE (0.05
CONCLUSION
Including AFE in the diet of dairy cows may alter the microbial composition of the rumen; however its effect on nutrient digestibility remains to be determined.
PubMed: 28183168
DOI: 10.5713/ajas.16.0839 -
Microorganisms Dec 2019Recurrent aphthous stomatitis (RAS) is the most common disease of the oral mucosa, and it has been recently associated with bacterial and fungal dysbiosis. To study this...
Recurrent aphthous stomatitis (RAS) is the most common disease of the oral mucosa, and it has been recently associated with bacterial and fungal dysbiosis. To study this link further, we investigated microbial shifts during RAS manifestation at an ulcer site, in its surroundings, and at an unaffected site, compared with healed mucosa in RAS patients and healthy controls. We sampled microbes from five distinct sites in the oral cavity. The one site with the most pronounced differences in microbial alpha and beta diversity between RAS patients and healthy controls was the lower labial mucosa. Detailed analysis of this particular oral site revealed strict association of the genus with healed mucosa of RAS patients, whereas the class Clostridia and genera , , , and were associated with the presence of an active ulcer. Furthermore, active ulcers were dominated by , which were negatively correlated with and and positively correlated with species. In addition, RAS patients showed increased serum levels of IgG against compared with healthy controls. Our study demonstrates that the composition of bacteria and fungi colonizing healthy oral mucosa is changed in active RAS ulcers, and that this alteration persists to some extent even after the ulcer is healed.
PubMed: 31805744
DOI: 10.3390/microorganisms7120636 -
Animals : An Open Access Journal From... Aug 2022This study investigated the effect of dietary Macleaya cordata extract (MCE) supplementation on the growth performance, serum parameters, and intestinal microbiota of...
This study investigated the effect of dietary Macleaya cordata extract (MCE) supplementation on the growth performance, serum parameters, and intestinal microbiota of yellow-feather broilers under heat stress. A total of 216 yellow-feather broilers (28-days-old) were randomly allotted into three groups. A control group (CON) (24 ± 2 °C) and heat stress group (HS) (35 ± 2 °C) received a basal diet, and heat-stressed plus MCE groups (HS-MCE) (35 ± 2 °C) were fed the basal diet with 1000 mg/kg MCE for 14 consecutive days. The results revealed that MCE supplementation improved the final body weight, average daily feed intake, average daily gain, and spleen index when compared with the HS group (p < 0.05). In addition, MCE supplementation decreased (p < 0.05) the activities of aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, and creatinine, and increased (p < 0.05) the glucose level and alkaline phosphatase activity in heat-stressed yellow-feathered broilers. Moreover, MCE treatment alleviated heat-stress-induced intestinal flora disturbances, decreased the Bacteroidota and Bacteroides relative abundances, and increased Firmicutes. A linear discriminant analysis effect size analysis found five differentially abundant taxa in the HS-MCE group, including Alistipes, Rikenellaceae, Mogibacterium, Butyrivibrio, and Lachnospira. These results suggest that MCE can alleviate HS-induced decline in growth performance by modulating blood biochemical markers and cecal flora composition in broilers.
PubMed: 36077916
DOI: 10.3390/ani12172197