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Yonsei Medical Journal Jan 2015We report three cases of recently named Bacteroides spp. isolates, two B. faecis isolates and one B. intestinalis isolate from clinical specimens of inpatients at a...
We report three cases of recently named Bacteroides spp. isolates, two B. faecis isolates and one B. intestinalis isolate from clinical specimens of inpatients at a Korean tertiary-care hospital in 2011. All isolates were susceptible to piperacillin-tazobactam, imipenem, meropenem, chloramphenicol, and metronidazole.
Topics: Aged; Anti-Bacterial Agents; Bacteroides; Female; Humans; Intestines; Male; Microbial Sensitivity Tests; Middle Aged
PubMed: 25510777
DOI: 10.3349/ymj.2015.56.1.292 -
Nature Medicine Aug 2021Treatment with combined immune checkpoint blockade (CICB) targeting CTLA-4 and PD-1 is associated with clinical benefit across tumor types, but also a high rate of...
Treatment with combined immune checkpoint blockade (CICB) targeting CTLA-4 and PD-1 is associated with clinical benefit across tumor types, but also a high rate of immune-related adverse events. Insights into biomarkers and mechanisms of response and toxicity to CICB are needed. To address this, we profiled the blood, tumor and gut microbiome of 77 patients with advanced melanoma treated with CICB, with a high rate of any ≥grade 3 immune-related adverse events (49%) with parallel studies in pre-clinical models. Tumor-associated immune and genomic biomarkers of response to CICB were similar to those identified for ICB monotherapy, and toxicity from CICB was associated with a more diverse peripheral T-cell repertoire. Profiling of gut microbiota demonstrated a significantly higher abundance of Bacteroides intestinalis in patients with toxicity, with upregulation of mucosal IL-1β in patient samples of colitis and in pre-clinical models. Together, these data offer potential new therapeutic angles for targeting toxicity to CICB.
Topics: Animals; CTLA-4 Antigen; Cell Line, Tumor; Female; Gastrointestinal Microbiome; Humans; Interleukin-1beta; Melanoma; Mice; Mice, Inbred C57BL; Programmed Cell Death 1 Receptor
PubMed: 34239137
DOI: 10.1038/s41591-021-01406-6 -
International Journal of Systematic and... Jan 2006During studies of the microbiota of human faeces, five strains of Gram-negative anaerobic rods were isolated following growth in a polyamine-deficient medium. These...
During studies of the microbiota of human faeces, five strains of Gram-negative anaerobic rods were isolated following growth in a polyamine-deficient medium. These strains belonged to the genus Bacteroides on the basis of 16S rRNA gene sequence data. 16S rRNA gene sequence similarity between one of the strains, 341T, and recognized species within the genus Bacteroides was <95 %. The DNA G+C content (44 mol%) and major fatty acid composition (anteiso-C(15 : 0), 32.0 %) supported the affiliation of strain 341(T) to the genus Bacteroides. Biochemical tests and DNA-DNA hybridization analysis demonstrated that strain 341T was distinct from Bacteroides uniformis and Bacteroides helcogenes, to which it was related most closely. On the basis of these data, a novel Bacteroides species, Bacteroides intestinalis sp. nov., is proposed with strain 341T (= JCM 13265T = DSM 17393T) as the type strain.
Topics: Bacteroides; Base Composition; Culture Media; Fatty Acids; Feces; Humans; Molecular Sequence Data; Polyamines; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Homology, Nucleic Acid; Species Specificity
PubMed: 16403880
DOI: 10.1099/ijs.0.63914-0 -
Microorganisms May 2021spp. of the human colonic microbiome degrade complex arabinoxylans from dietary fiber and release ferulic acid. Several studies have demonstrated the beneficial effects...
spp. of the human colonic microbiome degrade complex arabinoxylans from dietary fiber and release ferulic acid. Several studies have demonstrated the beneficial effects of ferulic acid. Here, we hypothesized that ferulic acid or the ferulic acid-rich culture supernatant of , cultured in the presence of complex arabinoxylans, enhances the immune response. Ferulic acid and the culture supernatant of bacteria cultured in the presence of insoluble arabinoxylans significantly decreased the expression of tumor necrosis factor-α and increased the expression of interleukin-10 and transforming growth factor β1 from activated dendritic cells compared to controls. The number of granulocytes in mesenteric lymph nodes, the number of spleen monocytes/granulocytes, and interleukin-2 and interleukin-12 plasma levels were significantly increased in mice treated with ferulic acid or the culture supernatant of bacteria cultured with insoluble arabinoxylans. Ferulic acid or the culture supernatant of bacteria cultured with insoluble arabinoxylans increased the expression of interleukin-12, interferon-α, and interferon-β in intestinal epithelial cell lines. This study shows that ferulic acid or the ferulic acid-rich culture supernatant of the colonic bacterium , cultured with insoluble arabinoxylans, exerts anti-inflammatory activity in dendritic cells under inflammatory conditions and enhances the Th1-type immune response under physiological conditions in mice.
PubMed: 34067445
DOI: 10.3390/microorganisms9061126 -
Scientific Reports Sep 2016Many human diets contain arabinoxylan, and the ease of genome sequencing coupled with reduced cost have led to unraveling the arsenal of genes utilized by the colonic...
Many human diets contain arabinoxylan, and the ease of genome sequencing coupled with reduced cost have led to unraveling the arsenal of genes utilized by the colonic Bacteroidetes to depolymerize this polysaccharide. The colonic Bacteroidetes with potential to ferment arabinoxylans include Bacteroides intestinalis. In this study, we analyzed the hydrolytic activities of members of a xylan degradation cluster encoded on the genome of Bacteroides intestinalis DSM 17393. Here, it is demonstrated that a cocktail of the xylanolytic enzymes completely hydrolyze arabinoxylans found in human diets. We show that this bacterium and relatives have evolved and secrete a unique bifunctional endoxylanase/arabinofuranosidase in the same polypeptide. The bifunctional enzyme and other secreted enzymes attack the polysaccharides extracellularly to remove the side-chains, exposing the xylan backbone for cleavage to xylo-oligosaccharides and xylose. These end products are transported into the cell where a β-xylosidase cleaves the oligosaccharides to fermentable sugars. While our experiments focused on B. intestinalis, it is likely that the extracellular enzymes also release nutrients to members of the colonic microbial community that practice cross-feeding. The presence of the genes characterized in this study in other colonic Bacteroidetes suggests a conserved strategy for energy acquisition from arabinoxylan, a component of human diets.
PubMed: 27681607
DOI: 10.1038/srep34360 -
BMC Biology Aug 2021The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of...
BACKGROUND
The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals.
RESULTS
Here we show that rapid phase variation of alternate capsular polysaccharides in Bacteroides intestinalis cultures plays an important role in a dynamic equilibrium between phage sensitivity and resistance, allowing phage and bacteria to multiply in parallel. The data also suggests the role of a concomitant phage persistence mechanism associated with delayed lysis of infected cells, similar to carrier state infection. From an ecological and evolutionary standpoint, this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other "benign" forms of phage infection when the host is stably present at high abundance.
CONCLUSION
Long-term persistence of bacteriophage and host could result from mutually beneficial mechanisms driving bacterial strain-level diversity and phage survival in complex environments.
Topics: Bacteria; Bacteriophages; Bacteroides; Humans; Phase Variation; Phylogeny
PubMed: 34407825
DOI: 10.1186/s12915-021-01084-3 -
Nature May 2023CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences....
CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss001, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.
Topics: Humans; Capsid; Cryoelectron Microscopy; DNA Viruses; Virion; Virus Assembly; Intestines; Viral Proteins; Protein Unfolding; Protein Folding
PubMed: 37138077
DOI: 10.1038/s41586-023-06019-2 -
Journal of Agricultural and Food... Apr 2022A novel enzyme Bi76 comprising GH10, E_set_Esterase_N, and CE1 modules was identified, with the highest homology (62.9%) with a bifunctional endoxylanase/feruloyl...
A novel enzyme Bi76 comprising GH10, E_set_Esterase_N, and CE1 modules was identified, with the highest homology (62.9%) with a bifunctional endoxylanase/feruloyl esterase among characterized enzymes. Interestingly, Bi76 hydrolyzed glucan substrates besides xylans and feruloylated substrates, suggesting that it is the first characterized trifunctional endoxylanase/endoglucanase/feruloyl esterase. Analyses of truncation variants revealed that GH10 and E_set_Esterase_N + CE1 modules encoded endoxylanase/endoglucanase and feruloyl esterase activities, respectively. Synergism analyses indicated that endoxylanase, α-l-arabinofuranosidase, and feruloyl esterase acted cooperatively in releasing ferulic acid (FA) and xylooligosaccharides from feruloylated arabinoxylan. The interdomain synergism of Bi76 overmatched the intermolecular synergism of TM1 and TM2. Importantly, Bi76 exhibited good capacity in producing FA, releasing 5.20, 4.38, 2.12, 1.35, 0.46, and 0.19 mg/g from corn bran, corn cob, wheat bran, corn stover, rice husk, and rice bran, respectively. This study expands the trifunctional endoxylanase/endoglucanase/feruloyl esterase repertoire and demonstrates the great potential of Bi76 in agricultural residue utilization.
Topics: Bacteroides; Carboxylic Ester Hydrolases; Cellulase; Coumaric Acids; Endo-1,4-beta Xylanases; Humans; Xylans
PubMed: 35316064
DOI: 10.1021/acs.jafc.2c01019 -
Cancer Discovery Sep 2021In patients with melanoma and in in vivo models, gut colonization by Bacteroides intestinalis is associated with increased immune-related adverse events, such as...
In patients with melanoma and in in vivo models, gut colonization by Bacteroides intestinalis is associated with increased immune-related adverse events, such as colitis, resulting from treatment with combined immune checkpoint blockade.
PubMed: 34373264
DOI: 10.1158/2159-8290.CD-NB2021-0371 -
The Journal of Allergy and Clinical... Dec 2023The composition of the gut microbiome has been associated with development of atopic conditions such as food allergy (FA) and asthma. African American or Black children...
BACKGROUND
The composition of the gut microbiome has been associated with development of atopic conditions such as food allergy (FA) and asthma. African American or Black children with FA have higher rate of asthma compared to their White counterparts.
OBJECTIVE
We sought to investigate whether the diversity and relative abundance (RA) of gut microbiota is different between children with FA from different racial backgrounds living in the same cities. Furthermore, we aimed to understand whether the difference in the gut microbiota is associated with asthma in children with FA.
METHODS
We analyzed and compared the stool microbiome of a cohort of Black and White children with FA by shotgun genomic sequencing.
RESULTS
A total of 152 children with IgE-mediated FA enrolled onto FORWARD (Food Allergy Outcomes Related to White and African American Racial Differences); 30 Black and 122 White children were included. The RA of several bacteria was associated with race and asthma. Most notably the RA of Bacteroides thetaiotaomicron, Chlamydia thrachomatis, Parabacteroides goldsteinii, and Bacteroides eggerthii were significantly higher, while the RA of Bifidobacterium sp CAG:754, Parabacterium johnsonii, Bacteroides intestinalis, and Bifidobacterium breve were significantly lower in stool samples of Black children compared to White children. Asthma was associated with lower RA of B breve, Bifidobacterium catenulatum, Prevotella copri, Veilloella sp CAG:933, and Bacteroides plebius, and higher RA of 3 Bacteroides species.
CONCLUSIONS
The observed variations in the gut microbiota of Black and White children such as differences in the Bacteroides and Bifidobacterium species along with their association to history of asthma in our cohort is indicative of their potential role in the higher rate of asthma observed among Black children with FA.
Topics: Child; Humans; Gastrointestinal Microbiome; Food Hypersensitivity; Microbiota; Feces; Asthma
PubMed: 37714436
DOI: 10.1016/j.jaci.2023.07.024