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Scientific Reports Feb 2019Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive...
Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive demographic and phylogeographic research, little is known about the composition of its gut microbiota and how it might vary based on potential environmental or host factors. We analysed the intestinal and faecal microbiota of 3 hare populations by Illumina MiSeq 16S rRNA gene amplicon sequencing. The phyla and OTU abundance composition differed significantly between intestinal and faecal samples (PERMANOVA: P = 0.002 and P = 0.031, respectively), but in both sample types Firmicutes and Bacteroidetes dominated the microbial community composition (45.51% and 19.30% relative abundance). Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71-fold change, P < 0.001). At OTU level, a significant enrichment with best BLAST hits to the Escherichia-Shigella group, Eubacterium limosum, Sphingomonas kyeonggiensis, Flintibacter butyricus and Blautia faecis were detected in intestinal samples (P < 0.05). In our statistical model, geographic location and possibly associated environmental factors had a greater impact on the microbiota composition than host factors. Population had a significant effect on the composition of abundant intestinal and faecal OTUs, and on the abundance of potential pathogenic bacteria of the family Enterobacteriaceae, regularly associated with intestinal dysbiosis in hares, in faecal samples. Our study is the first to describe the microbiota in brown hares and provides a foundation to generate hypothesis aiming to test the role of gut health in population fluctuations of the species.
Topics: Animals; Bacteria; Bacteroidetes; Feces; Female; Firmicutes; Gastrointestinal Microbiome; Hares; Male; RNA, Ribosomal, 16S
PubMed: 30804494
DOI: 10.1038/s41598-019-39638-9 -
Glycobiology Jun 2021The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these...
The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these are adept at scavenging host glycans within this environment, including mucin O-linked glycans, N-linked glycoproteins and highly sulfated glycosaminoglycans (GAGs) such as heparin (Hep) and chondroitin sulfate (CS). Several recent biochemical studies have revealed the specific polysaccharide utilization loci (PULs) within the model symbiont Bacteroides thetaiotaomicron for the deconstruction of these host glycans. Here we discuss the Sus-like paradigm that defines glycan uptake by the Bacteroidetes and the salient details of the PULs that target heparin/heparan sulfate (HS) and chondroitin sulfate/dermatan sulfate (DS)/hyaluronic acid (HA), respectively, in B. thetaiotaomicron. The ability of the Bacteroidetes to target highly sulfated host glycans is key to their success in the gut environment but can lead to inflammation in susceptible hosts. Therefore, our continued understanding of the molecular strategies employed by these bacteria to scavenge carbohydrate nutrition is likely to lead to novel ways to alter their metabolism to promote host health.
Topics: Bacteroides; Bacteroides thetaiotaomicron; Bacteroidetes; Glycosaminoglycans; Heparitin Sulfate; Humans; Polysaccharides
PubMed: 32518945
DOI: 10.1093/glycob/cwaa054 -
MSphere Mar 2019A gnotobiotic (chicken) model was developed to study the dynamics of intestinal microflora from hatching to 18 days of age employing metagenomics. Intestinal samples...
A gnotobiotic (chicken) model was developed to study the dynamics of intestinal microflora from hatching to 18 days of age employing metagenomics. Intestinal samples were collected from a local population of feral chickens and administered orally to germfree 3-day-old chicks. Animals were euthanized on days 9 and 18 postinoculation, and intestinal samples were collected and subjected to metagenomic analysis. On day 18, the five most prevalent phyla were (43.03 ± 3.19%), (38.51 ± 2.67%), (6.77 ± 0.7%), (6.38 ± 0.7%), and (2.71 ± 0.55%). Principal-coordinate analysis showed that the day 18 variables clustered more closely than the day 9 variables, suggesting that the microbial communities had changed temporally. The Morista-Horn index values ranged from 0.7 to 1, indicating that the communities in the inoculum and in the day 9 and day 18 samples were more similar than dissimilar. The predicted functional profiles of the microbiomes of the inoculum and the day 9 and day 18 samples were also similar (values of 0.98 to 1). These results indicate that the gnotobiotic chicks stably maintained the phylogenetic diversity and predicted metabolic functionality of the inoculum community. The domestic chicken is the cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year. It serves as an economically valuable source of protein globally. The microbiome of poultry has important effects on chicken growth, feed conversion, immune status, and pathogen resistance. The aim of our research was to develop a gnotobiotic chicken model appropriate for the study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse sets of gut bacteria. Therefore, besides the use of this model to study mechanisms of gut microbiota interactions in the chicken gut, it could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.
Topics: Animals; Bacteria; Bacteroidetes; Chickens; DNA, Bacterial; Firmicutes; Gastrointestinal Microbiome; Gastrointestinal Tract; Germ-Free Life; Host Microbial Interactions; Metagenomics; Phylogeny; Principal Component Analysis; RNA, Ribosomal, 16S
PubMed: 30918057
DOI: 10.1128/mSphere.00035-19 -
Journal of Dental Research Jun 2016In recent years, several new periodontal taxa have been associated with the etiology of periodontitis. A recent systematic review provides further support for the...
In recent years, several new periodontal taxa have been associated with the etiology of periodontitis. A recent systematic review provides further support for the pathogenic role of 17 species/phylotypes. Thus, the aim of this study was to assess the prevalence and levels of these species in subjects with generalized chronic periodontitis (GChP; n = 30), generalized aggressive periodontitis (GAgP; n = 30), and periodontal health (PH; n = 30). All subjects underwent clinical and microbiological assessment. Nine subgingival plaque samples were collected from each subject and analyzed for their content of 20 bacterial species/phylotypes through the RNA-oligonucleotide quantification technique. Subjects from the GChP and GAgP groups presented the highest mean values for all clinical parameters in comparison with the PH group (P < 0.05). Subjects with GChP and GAgP showed significantly higher mean levels of Bacteroidetes sp. human oral taxon (HOT) 274, Fretibacterium sp. HOT 360, and TM7 sp. HOT 356 phylotypes, as well as higher mean levels of Filifactor alocis, Fretibacterium fastidiosum, Porphyromonas gingivalis, Tannerella forsythia, and Selenomonas sputigena species than PH subjects (P < 0.05). GAgP subjects presented higher mean levels of TM7 sp. HOT 356 and F. alocis than GChP subjects (P < 0.05). A significantly higher mean prevalence of Bacteroidales sp. HOT 274, Desulfobulbus sp. HOT 041, Fretibacterium sp. HOT 360, and Fretibacterium sp. HOT 362 was found in subjects with GChP and GAgP than in PH subjects. Mean levels of P. gingivalis (r = 0.68), T. forsythia (r = 0.62), F. alocis (r = 0.51, P = 0.001), and Fretibacterium sp. HOT 360 (r = 0.41) were correlated with pocket depth (P < 0.001). In conclusion, Bacteroidales sp. HOT 274, Desulfobulbus sp. HOT 041, Fretibacterium sp. HOT 360, Fretibacterium sp. HOT 362, and TM7 sp. HOT 356 phylotypes, in addition to F. alocis, F. fastidiosum, and S. sputigena, seem to be associated with periodontitis, and their role in periodontal pathogenesis should be further investigated.
Topics: Aggressive Periodontitis; Bacteria; Bacteroides; Bacteroidetes; Biofilms; Chronic Periodontitis; Dental Plaque; Humans; Microbiota
PubMed: 26936213
DOI: 10.1177/0022034516634619 -
Scientific Reports Sep 2018Bowel obstruction (OB) causes local and systemic dysfunctions. Here we investigated whether obstruction leads to alterations in microbiota community composition and...
Bowel obstruction (OB) causes local and systemic dysfunctions. Here we investigated whether obstruction leads to alterations in microbiota community composition and total abundance, and if so whether these changes contribute to dysfunctions in OB. Partial colon obstruction was maintained in rats for 7 days. The mid colon and its intraluminal feces - proximal to the obstruction - were studied. OB did not cause bacterial overgrowth or mucosa inflammation, but induced profound changes in fecal microbiota composition and diversity. At the phylum level, the 16S rRNA sequencing showed a significant decrease in the relative abundance of Firmicutes with corresponding increases in Proteobacteria and Bacteroidetes in OB compared with sham controls. Daily treatment using broad spectrum antibiotics dramatically reduced total bacterial abundance, but increased the relative presence of Proteobacteria. Antibiotics eliminated viable bacteria in the spleen and liver, but not in the mesentery lymph node in OB. Although antibiotic treatment decreased muscle contractility in sham rats, it had little effect on OB-associated suppression of muscle contractility or inflammatory changes in the muscle layer. In conclusion, obstruction leads to marked dysbiosis in the colon. Antibiotic eradication of microbiota had limited effects on obstruction-associated changes in inflammation, motility, or bacterial translocation.
Topics: Animals; Anti-Bacterial Agents; Bacterial Translocation; Bacterial Typing Techniques; Bacteroidetes; Colon; Dysbiosis; Feces; Firmicutes; Gastrointestinal Microbiome; Intestinal Obstruction; Liver; Lymph Nodes; Male; Phylogeny; Proteobacteria; RNA, Ribosomal, 16S; Rats; Rats, Sprague-Dawley; Spleen
PubMed: 30177854
DOI: 10.1038/s41598-018-31033-0 -
Gut Microbes 2011It is becoming increasingly clear that diet is one of the major factors that drives the function and composition of the intestinal microbiota. The diet of humans is... (Review)
Review
It is becoming increasingly clear that diet is one of the major factors that drives the function and composition of the intestinal microbiota. The diet of humans is highly diverse when considering different populations or even a single individual over a relatively short period of time. However, we are just beginning to understand the mechanisms that connect dietary change to intestinal microbiota dynamics. The community of microbes within our distal digestive tract influences numerous aspects of our biology, and aberrant shifts in its composition appear to be associated with several diseases. It is, therefore, necessary to understand how our behaviour and environmental factors, such as changes in diet, impact our intestinal residents. Here we look to recent work to highlight some of the major questions on the horizon for understanding the key role that the Bacteroidetes play in the commerce of dietary polysaccharides within the intestine.
Topics: Bacteroidetes; Gastrointestinal Tract; Humans; Models, Biological; Polysaccharides
PubMed: 21637023
DOI: 10.4161/gmic.2.2.15232 -
Infection and Immunity Jan 2015Capnocytophaga canimorsus, a dog mouth commensal and a member of the Bacteroidetes phylum, causes rare but often fatal septicemia in humans that have been in contact...
Capnocytophaga canimorsus, a dog mouth commensal and a member of the Bacteroidetes phylum, causes rare but often fatal septicemia in humans that have been in contact with a dog. Here, we show that C. canimorsus strains isolated from human infections grow readily in heat-inactivated human serum and that this property depends on a typical polysaccharide utilization locus (PUL), namely, PUL3 in strain Cc5. PUL are a hallmark of Bacteroidetes, and they encode various products, including surface protein complexes that capture and process polysaccharides or glycoproteins. The archetype system is the Bacteroides thetaiotaomicron Sus system, devoted to starch utilization. Unexpectedly, PUL3 conferred the capacity to acquire iron from serotransferrin (STF), and this capacity required each of the seven encoded proteins, indicating that a whole Sus-like machinery is acting as an iron capture system (ICS), a new and unexpected function for Sus-like machinery. No siderophore could be detected in the culture supernatant of C. canimorsus, suggesting that the Sus-like machinery captures iron directly from transferrin, but this could not be formally demonstrated. The seven genes of the ICS were found in the genomes of several opportunistic pathogens from the Capnocytophaga and Prevotella genera, in different isolates of the severe poultry pathogen Riemerella anatipestifer, and in strains of Bacteroides fragilis and Odoribacter splanchnicus isolated from human infections. Thus, this study describes a new type of ICS that evolved in Bacteroidetes from a polysaccharide utilization system and most likely represents an important virulence factor in this group.
Topics: Bacteroidetes; Gram-Negative Bacterial Infections; Humans; Iron; Membrane Transport Proteins; Multigene Family; Serum
PubMed: 25368114
DOI: 10.1128/IAI.02042-14 -
Microbiology Spectrum Aug 2023Bacteria have to persist under low iron conditions in order to adapt to the nutritional immunity of a host. Since the knowledge of iron stimulon of is sparse, we...
Bacteria have to persist under low iron conditions in order to adapt to the nutritional immunity of a host. Since the knowledge of iron stimulon of is sparse, we examined oral (Porphyromonas gingivalis and Prevotella intermedia) and gut (Bacteroides thataiotaomicron) representatives for their ability to adapt to iron deplete and iron replete conditions. Our transcriptomics and comparative genomics analysis show that many iron-regulated mechanisms are conserved within the phylum. They include genes upregulated in low iron, as follows: (flavodoxin), (hemin uptake operon), and loci encoding ABC transporters. Downregulated genes were (ferredoxin), (rubrerythrin), (succinate dehydrogenase/fumarate reductase), (oxoglutarate oxidoreductase/dehydrogenase), and (pyruvate:ferredoxin/flavodoxin oxidoreductase). Some genus-specific mechanisms, such as the of B. thetaiotaomicron coding for carbohydrate metabolism and the coding for xenosiderophore utilization were also identified. While all bacteria tested in our study had the operon coding for nitrite reduction and were able to reduce nitrite levels present in culture media, the expression of the operon was iron dependent only in B. thetaiotaomicron. It is noteworthy that we identified a significant overlap between regulated genes found in our study and the B. thetaiotaomicron colitis study (W. Zhu, M. G. Winter, L. Spiga, E. R. Hughes et al., Cell Host Microbe 27:376-388, 2020, http://dx.doi.org/10.1016/j.chom.2020.01.010). Many of those commonly regulated genes were also iron regulated in the oral bacterial genera. Overall, this work points to iron being the master regulator enabling bacterial persistence in the host and paves the way for a more generalized investigation of the molecular mechanisms of iron homeostasis in . are an important group of anaerobic bacteria abundant both in the oral and gut microbiomes. Although iron is a required nutrient for most living organisms, the molecular mechanisms of adaptation to the changing levels of iron are not well known in this group of bacteria. We defined the iron stimulon of by examination of the transcriptomic response of Porphyromonas gingivalis and Prevotella intermedia (both belong to the oral microbiome) and Bacteroidetes thetaiotaomicron (belongs to the gut microbiome). Our results indicate that many of the iron-regulated operons are shared among the three genera. Furthermore, using bioinformatics analysis, we identified a significant overlap between our studies and transcriptomic data derived from a colitis study, thus underscoring the biological significance of our work. Defining the iron-dependent stimulon of can help to identify the molecular mechanisms of iron-dependent regulation as well as better understand the persistence of the anaerobes in the human host.
Topics: Humans; Bacteroidetes; Ferredoxins; Flavodoxin; Nitrites; Porphyromonas gingivalis; Iron; Iron Deficiencies; Colitis; Inflammation
PubMed: 37314331
DOI: 10.1128/spectrum.04733-22 -
European Review For Medical and... Dec 2023This systematic review examines the effectiveness of diode laser irradiation in reducing the levels of red complex bacteria as well as periodontal parameters of pocket...
OBJECTIVE
This systematic review examines the effectiveness of diode laser irradiation in reducing the levels of red complex bacteria as well as periodontal parameters of pocket depth and clinical attachment level.
MATERIALS AND METHODS
We conducted electronic searches across databases such as Scopus, Embase, Medline, and Web of Science databases in July 2022. Randomized controlled trials that evaluated the reduction of red-complex bacteria in patients with periodontitis using diode lasers were included. The primary focus was the reduction in the microbial count of red complex bacteria, whereas probing depth and attachment level were considered secondary outcomes. Articles in languages other than English were excluded. Study quality was assessed based on the Cochrane Handbook for Systematic Reviews of Interventions and the ROB2 tool.
RESULTS
After searching the databases, eight independent studies were included, with a sample size of 210 subjects. The average age group of the study population was 30-60 years, and there was a lack of consensus on the antimicrobial effect of diode lasers. Out of the eight studies, four studies reported no significant difference in the levels of red complex bacteria before and after laser application. Three studies reported significantly lower levels of red complex bacteria in the intergroup comparison. One study reported that laser had no significant effect on intergroup bacterial levels. The combination of diode laser irradiation with scaling reduced the count of red complex bacteria and improved the clinical parameters, although not significantly.
CONCLUSIONS
Based on the limited evidence available, the adjunctive use of diode laser for scaling and root planning may provide some additional benefit in terms of reduction of red complex bacterial count and clinical parameters. Further well-designed trials and the use of objective measures are necessary before outlining universal guidelines for best practice. The adjunctive use of diode laser in non-surgical periodontal therapy may provide a reduction in the red complex microbial count and improvement in clinical parameters, decreasing the need for periodontal surgery.
Topics: Adult; Humans; Middle Aged; Bacterial Load; Chronic Periodontitis; Lasers, Semiconductor; Systematic Reviews as Topic; Bacteroidetes; Tannerella
PubMed: 38164844
DOI: 10.26355/eurrev_202312_34779 -
Cell Reports Dec 2021The functional and genomic diversity of the human gut microbiome is shaped by horizontal transfer of mobile genetic elements (MGEs). Characterized MGEs can encode genes...
The functional and genomic diversity of the human gut microbiome is shaped by horizontal transfer of mobile genetic elements (MGEs). Characterized MGEs can encode genes beneficial for their host's self-defense (e.g., antibiotic resistance) or ability to compete for essential or limited resources (e.g., vitamins). Vitamin B and related compounds (corrinoids) are critical nutrients that enable colonization by members of the common gut microbe phylum, the Bacteroidetes. Herein, we identify a distinct class of MGEs in the Bacteroidetes responsible for the mobilization and exchange of the genes required for transport of corrinoids, a group of cyclic tetrapyrrole cofactors including vitamin B (btuGBFCD). This class includes two distinct groups of conjugative transposons (CTns) and one group of phage. Conjugative transfer and vitamin B transport activity of two of the CTns were confirmed in vitro and in vivo, demonstrating the important role MGEs play in distribution of corrinoid transporters in the Bacteroidetes.
Topics: Animals; Bacterial Proteins; Bacteroidetes; Corrinoids; Female; Gastrointestinal Microbiome; Humans; Interspersed Repetitive Sequences; Male; Membrane Transport Proteins; Mice; Mice, Inbred C57BL; Vitamin B 12; Vitamin B Complex
PubMed: 34965410
DOI: 10.1016/j.celrep.2021.110164