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Purpose: The intestine has substantial role in cholesterol homeostasis due to the presence of various cholesterol transporters and gut microbiota. Bacteroides spp. are important members of gut microbiota that employ outer membrane vesicles (OMVs) to interact with host. In this regard, we evaluated the effect of Bacteroides fragilis, Bacteroides thetaiotaomicron and related OMVs on the gene expression of important cholesterol transporters, Niemann-Pick C1-Like 1 (NPC1L1), ATP-binding cassette (ABCA1), and liver X receptors (LXRs) in Caco-2 cells. Methods: OMVs were isolated from overnight brain heart infusion (BHI) broth of bacterial standard strains using deoxycholate and assessed by Scanning electron microscopy (SEM). The relative change in genes expression was assessed by Quantitative reverse transcription PCR (RT-qPCR) based on SYBR Green and 2-∆∆ct method in Caco-2 cells that were treated with bacteria and OMVs. Data were statistically analyzed with GraphPad Prism software. Finally, pathway enrichment based on the studied genes was performed using Cytoscape plugin ClueGO. Results: B. fragilis (P value = 0.002) and B. thetaiotaomicron (P value = 0.001) significantly reduced NPC1L1 gene expression in Caco-2 cells. Interestingly, NPC1L1 transcripts were significantly increased by both OMVs(P value = 0.04) (P value = 0.01). Also, LXRβ was significantly down regulated by B. thetaiotaomicron (P value = 0.02). ClueGO analysis on the studied genes demonstrated several functional groups which involve in lipid and cholesterol metabolism. Conclusion: The opposite effect of B. fragilis, B. thetaiotaomicron and related OMVs on the NPC1L1 gene expression was observed in Caco-2 cells. Interestingly, these effects partially were in line with the alternation of LXRs expression. However, based on pathway enrichment analysis, further molecular investigations are required to elaborate in details the specific association between Bacteroides spp. and OMVs with regulation of cholesterol signaling pathways including cholesterol transport, lipid storage, lipid homeostasis and cholesterol homeostasis. [ABSTRACT FROM AUTHOR]

Macropod progressive periodontal disease (MPPD) is a necrotizing, polymicrobial, inflammatory disease commonly diagnosed in captive macropods. MPPD is characterized by gingivitis associated with dental plaque formation, which progresses to periodontitis and then to osteomyelitis of the mandible or maxilla. However, the underlying microbial causes of this disease remain poorly understood. In this study, we collected 27 oral plaque samples and associated clinical records from 22 captive Macropodidae and Potoroidae individuals that were undergoing clinical examination at Adelaide and Monarto Zoos in South Australia (15 healthy, 7 gingivitis and 5 periodontitis-osteomyelitis samples). The V3-V4 region of the 16S ribosomal RNA gene was sequenced using an Illumina Miseq to explore links between MPPD and oral bacteria in these animals. Compositional differences were detected between the microbiota of periodontitis-osteomyelitis cases compared to healthy samples (p-value with Bonferroni correction < 0.01), as well as gingivitis cases compared to healthy samples (p-value with Bonferroni correction < 0.05) using Permutational Multivariate Analysis of Variance (PERMANOVA). An overabundance of Porphyromonas, Fusobacterium, and Bacteroides taxa was also identified in animals with MPPD compared to healthy individuals using linear discriminant analysis effect size (LEfSe; p = < 0.05). An increased abundance of Desulfomicrobium also was detected in MPPD samples (LEfSe; p < 0.05), which could potentially reflect differences in disease progression. This is the first microbiota analysis of MPPD in captive macropods, and these results support a polymicrobial pathogenesis of MPPD, suggesting that the microbial interactions underpinning MPPD may be more complex than previously documented. [ABSTRACT FROM AUTHOR]

Pathogenic changes in gut microbial composition precede the onset of HIV-1 infection in men who have sex with men (MSM). This process is associated with increased levels of systemic inflammatory biomarkers and risk for AIDS development. Using mediation analysis framework, in this report we link the effects of unprotected receptive intercourse among MSM prior to primary HIV-1 infection to higher levels of proinflammatory cytokines sCD14 and sCD163 in plasma and a significant decrease in the abundance of A. muciniphila, B. caccae, B. fragilis, B. uniformis, Bacteroides spp., Butyricimonas spp., and Odoribacter spp., and a potential increase in the abundance of Dehalobacterium spp. and Methanobrevibacter spp. in stools of MSM with the highest number of sexual partners. These differences in microbiota, together with a reduction in the pairwise correlations among commensal and short-chain fatty acid-producing bacteria with a number of sexual partners, support an increase in gut dysbiosis with the number of sexual partners. These results demonstrate the interconnectedness of sexual behavior, immune response, and microbiota composition, notably among MSM participating in high-risk sexual behaviors. Sexual behavior among men who have receptive anal intercourse with men is linked to changes in the gut microbiome and systemic inflammation leading to HIV-1 infection. [ABSTRACT FROM AUTHOR]

A collection of 50 clinical isolates of Bacteroides was examined for plasmid deoxyribonucleic acid content. An attempt was then made to correlate the presence of plasmids with a specific phenotypic property. Of the 20 Bacteroides which contained plasmids, 18 were found to harbour plasmids of ≤ 9.8 megadaltons. The most common plasmid had a molecular weight of 4.8 megadaltons and was found in 9 strains. Most strains had multiple plasmid bands. All strains were examined for resistance to penicillin, cefoxitin, erythromycin, tetracycline, sulphamethoxazole, clindamycin, chloramphenicol, arsenate, silver, cadmium, mercury, chromium, lead, nickel and cobalt, and for the production of β-lactamase, heparinase, deoxyribonuclease, haemolysins and bacteriocins. Using a Chi-squared analysis, there was no statistically significant correlation between any of these phenotypic traits and the presence of plasmids, except bacteriocin production. A total of 15 out of 20 (75%) of plasmid-containing strains produced bacteriocins while only 10 out of 30 (33%) of plasmid-free strains were capable of bacteriocin production (χ², p < 0.005). Attempts to transfer or cure resistance to antibiotics and heavy metals or bacteriocin production were not successful. [ABSTRACT FROM AUTHOR]

CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications. [ABSTRACT FROM AUTHOR]

Fluorescence in situ hybridisation (FISH) is a powerful molecular technique that enables direct visualisation of specific bacterial species. Few studies have established FISH protocols for tonsil tissue in Carnoy's fixative, accordingly limiting its application to investigate the pathogenesis of tonsillar hyperplasia. Tonsil tissue from 24 children undergoing tonsillectomy for either recurrent tonsillitis or sleep-disordered breathing were obtained during a previous study. The specificity of each of the five FISH probes (Fusobacterium spp., Bacteroides spp., Streptococcus spp., Haemophilus influenzae and Pseudomonas spp.) were successfully optimised using pure and mixed bacterial isolates, and in Carnoy's fixed tonsil tissue. Bacteroides spp. were present in 100% of patients with microcolonies. In comparison, the prevalence of Fusobacterium spp. was 93.8%, Streptococcus spp. 85.7%, H. influenzae 82.35% and Pseudomonas spp. 76.5%. Notable differences in the organisation of bacterial taxa within a single microcolony were also observed. This is the first study to establish a robust FISH protocol identifying multiple aerobic and anaerobic bacteria in Carnoy's fixed tonsil tissue. This protocol provides a strong foundation for combining histological and microbiological analyses of Carnoy's fixed tonsil samples. It may also have important implications on the analysis of microorganisms in other human tissues prepared using the same techniques. [ABSTRACT FROM AUTHOR]

The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics. [ABSTRACT FROM AUTHOR]

Manure effluents (MEs) of livestock enterprises represent a rich nutrient medium for the development of various aerobic microorganisms (MOs). A wide range of odor-forming substances (OFSs) and greenhouse gases enter the atmosphere as a result of the biodegradation of the organic components of the MEs. The intensity and main directions of ME destruction depend on the composition and abundance of the microbiota. A solution of sodium hypochlorite can be used to suppress the processes of decomposition of the biogenic components of the MEs. In the process of research, it was found that the introduction of 0.005% active chlorine into the liquid ME fraction (pH 6.8; humidity 99.1%) leads to a decrease in the number of representatives of putrefactive microbiota such as Bacteroides spp., Clostridium spp., Escherichia coli, Pseudomonas spp., Sarcina ventriculi, and Peptostreptococcus anaerobius. The corresponding ammonifiers take an active part in the processes of biodegradation of organic substances, which result in the formation of acetic, isovaleric, butyric acids, indoles, skatoles, ammonia, hydrogen sulfide, mercaptans, etc. On the contrary, the amount of microbiota that does not make a significant contribution to the production of OFSs (Saccharomyces cerevisiae, Rhodotorula glutinis, Lactobacillus spp., etc.) increased. The number of some producers of volatile fatty acids (VFAs), like Anaerococcus prevotii, Acidaminococcus spp., Prevotella spp., etc., increased; however, they did not have a noticeable effect on the intensity and nature of the ME odor, which may be explained by the formation of nonvolatile VFA salts at pH above 7.0. The amount of Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella sp., Proteus spp., Alistipes putredinis, Bifidobacterium spp., Candida tropicalis, and Candida albicans practically did not change when NaOCl was added to the MEs. The total emission of gaseous substances, the main components of which are greenhouse gases CO2 and CH4, decreased by more than 17% as a result of the transformation of the microbiota. The intensity of the unpleasant odor was significantly reduced. The NaOCl solution can be used for ME treatment in manure tanks. The introduction of the practice of treating MEs with this biocide is facilitated by its availability, low cost, and safety for the environment. [ABSTRACT FROM AUTHOR]

Microbiota and immunity affect the host's susceptibility to SARS-CoV-2 infection and the severity of COVID-19. This study aimed to identify significant alterations in the microbiota composition, immune signaling pathways, their potential association, and candidate microRNA in COVID-19 patients using an in silico study model. Enrichment online databases and Python programming were utilized to analyze GSE164805, GSE180594, and GSE182279, as well as NGS data of microbiota composition (PRJNA650244 and PRJNA660302) associated with COVID-19, employing amplicon-based/marker gene sequencing methods. C1, TNF, C2, IL1, and CFH genes were found to have a significant impact on immune signaling pathways. Additionally, we observed a notable decrease in Bacteroides spp. and Faecalibacterium sp., while Escherichia coli, Streptococcus spp., and Akkermansia muciniphila showed increased abundance in COVID-19. Notably, A. muciniphila demonstrated an association with immunity through C1 and TNF, while Faecalibacterium sp. was linked to C2 and IL1. The correlation between E. coli and CFH, as well as IL1 and Streptococcus spp. with C2, was identified. hsa-let-7b-5p was identified as a potential candidate that may be involved in the interaction between the microbiota composition, immune response, and COVID-19. In conclusion, integrative in silico analysis shows that these microbiota members are potentially crucial in the immune responses against COVID-19. [ABSTRACT FROM AUTHOR]

Purpose: Impaired gut barrier function is associated with systemic inflammation and many chronic diseases. Undigested dietary proteins are fermented in the colon by the gut microbiota which produces nitrogenous metabolites shown to reduce barrier function in vitro. With growing evidence of sex-based differences in gut microbiotas, we determined whether there were sex by dietary protein interactions which could differentially impact barrier function via microbiota modification. Methods: Fermentation systems were inoculated with faeces from healthy males (n = 5) and females (n = 5) and supplemented with 0.9 g of non-hydrolysed proteins sourced from whey, fish, milk, soya, egg, pea, or mycoprotein. Microbial populations were quantified using fluorescence in situ hybridisation with flow cytometry. Metabolite concentrations were analysed using gas chromatography, solid phase microextraction coupled with gas chromatography-mass spectrometry and ELISA. Results: Increased protein availability resulted in increased proteolytic Bacteroides spp (p < 0.01) and Clostridium coccoides (p < 0.01), along with increased phenol (p < 0.01), p-cresol (p < 0.01), indole (p = 0.018) and ammonia (p < 0.01), varying by protein type. Counts of Clostridium cluster IX (p = 0.03) and concentration of p-cresol (p = 0.025) increased in males, while females produced more ammonia (p = 0.02), irrespective of protein type. Further, we observed significant sex-protein interactions affecting bacterial populations and metabolites (p < 0.005). Conclusions: Our findings suggest that protein fermentation by the gut microbiota in vitro is influenced by both protein source and the donor's sex. Should these results be confirmed through human studies, they could have major implications for developing dietary recommendations tailored by sex to prevent chronic illnesses. [ABSTRACT FROM AUTHOR]

Purpose: We investigated the clinical features of Bacteroides bacteremia for 5 years to determine the risk factors for mortality and to ascertain whether bacteremia due to Bacteroides spp. is associated with colorectal carcinoma. Methods: This study comprised a review of all patients with Bacteroides bacteremia at a teaching hospital in Tokyo from April 2003 to March 2008. We also conducted a case-control study between Bacteroides bacteremia and bacteremia due to other pathogens. Results: During the study period, 25 cases of bacteremia were due to Bacteroides spp. Bacteroides bacteremia was associated with a high mortality rate (24%). Malignancy (76%) was the major comorbidity, followed by a history of surgery (40%). Colorectal carcinoma was the most frequent ( n = 8, 32%) of the comorbid malignancies and was recognized as the primary infection site in six cases. Prevalence of colorectal carcinoma as comorbidity was significantly higher in Bacteroides bacteremia than in other bacteremia. Conclusions: In the Bacteroides bacteremia cases of this study, colorectal carcinoma was the major comorbidity and primary infection site. Colorectal carcinoma screening in Bacteroides bacteremia patients is potentially an important diagnostic marker for the early detection of this infection in the future. [ABSTRACT FROM AUTHOR]

Many factors underlie the development of inflammatory bowel disease (IBD) in humans. In particular, imbalance of microbiota and thinning of the mucosal layer in the large intestine play a huge role. Pathogenic microorganisms also exacerbate the course of diseases. In this research the role of mucin 2 deficiency in the formation of intestinal microflora in the experimental model using the Muc2 gene knockout mice in the presence of Helicobacter spp. was investigated. Also, restorative and anti-inflammatory effect of the dietary L-fucose in the Muc2–/– mice on microflora and immunity was evaluated. For this purpose, bacterial diversity in feces was studied in the animals before and after antibiotic therapy and role of the dietary L-fucose in their recovery was assessed. To determine the effect of bacterial imbalance and fucose on the immune system, mRNA levels of the genes encoding pro-inflammatory cytokines (Tnf, Il1a, Il1b, Il6) and transcription factors of T cells (Foxp3 – Treg, Rorc – Th17, Tbx21 – Th1) were determined in the colon tissue of the Muc2–/– mice. Significant elimination of bacteria due to antibiotic therapy caused decrease of the fucose levels in the intestine and facilitated reduction of the regulatory T cell transcription factor (Foxp3). When the dietary L-fucose was added to antibiotics, the level of bacterial DNA of Bacteroides spp. in the feces of the Muc2–/– mice was partially restored. T regulatory cells are involved in the regulation of inflammation in the Muc2–/– mice. Antibiotics reduced the number of regulatory T cell but did not decrease the inflammatory response to infection. Fucose, as a component of mucin 2, helped to maintain the level of Bacteroides spp. during antibiotic therapy of the Muc2–/– mice and restored biochemical parameters, but did not affect the inflammatory response. [ABSTRACT FROM AUTHOR]

The objective of this study was to evaluate the fermentation characteristics of proteins from diverse sources by human gut microbiota. Cereal proteins (rice and oat), red meat proteins (pork and beef), chicken protein and casein were selected as the substrates for simulated gastrointestinal digestion (SGID), and human faecal samples were collected from healthy donors as the inoculum of fermentation. In this study, we further analyzed the correlations of amino acids (AA) compositions, fermentation productions and gut microbiota. As the results, the animal protein groups had higher degree of hydrolysis (DH) after digestion and higher levels of ammonia nitrogen (NH3-N) after fermentation than cereal proteins. The pH value of fermentation liquid declined as proteins were added during fermentation. Cereal protein groups promoted the gut microbiota to produce more short chain fatty acids (SCFAs) with the high proportion of acetate, propionate and butyrate by lowering the pH than red meat proteins. The abundance of Firmicutes at phylum level in cereal protein groups was lower than red meat proteins after fermentation. The cereal protein groups enhanced the growth of Bacteroides spp. and Bifidobacterium spp. while red meat proteins stimulated the growth of Peptoclostridium spp.. Taken together, our research implies that cereal proteins have better fermentation characters than red meat proteins. [ABSTRACT FROM AUTHOR]

Vitamin B12 (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition for this keystone micronutrient is severe. Contrasting with Enterobacteria, members of the dominant genus Bacteroides often encode several BtuB vitamin B12 outer membrane transporters together with a conserved array of surface-exposed B12-binding lipoproteins. Here we show that the BtuB transporters from Bacteroides thetaiotaomicron form stable, pedal bin-like complexes with surface-exposed BtuG lipoprotein lids, which bind B12 with high affinities. Closing of the BtuG lid following B12 capture causes destabilisation of the bound B12 by a conserved BtuB extracellular loop, causing translocation of the vitamin to BtuB and subsequent transport. We propose that TonB-dependent, lipoprotein-assisted small molecule uptake is a general feature of Bacteroides spp. that is important for the success of this genus in colonising the human gut. Uptake of vitamin B12 is important for colonisation of the gut by Bacteroides species. Here the authors characterise B12 uptake in Bacteroides thetaiotaomicron, mediated by outer membrane protein complexes consisting of surface-exposed BtuG lipoproteins and BtuB TonB-dependent transporters. [ABSTRACT FROM AUTHOR]

Non-alcoholic steatohepatitis (NASH) is a more dangerous form of chronic non-alcoholic fatty liver disease (NAFLD). In the current investigation, the influence of citicoline on high-fat diet (HFD)-induced NASH was examined, both alone and in combination with Lactobacillus (probiotic). NASH was induced by feeding HFD (10% sugar, 10% lard stearin, 2% cholesterol, and 0.5% cholic acid) to rats for 13 weeks and received single i.p. injection of streptozotocin (STZ, 30 mg/kg) after 4 weeks. Citicoline was given at two dose levels (250 mg and 500 mg, i.p.) at the beginning of the sixth week, and in combination with an oral suspension of Lactobacillus every day for eight weeks until the study's conclusion. HFD/STZ induced steatohepatitis as shown by histopathological changes, elevated serum liver enzymes, serum hyperlipidemia and hepatic fat accumulation. Moreover, HFD convinced oxidative stress by increased lipid peroxidation marker (MDA) and decreased antioxidant enzymes (GSH and TAC). Upregulation of TLR4/NF-kB and the downstream inflammatory cascade (TNF-α, and IL-6) as well as Pentaraxin, fetuin-B and apoptotic markers (caspase-3 and Bax) were observed. NASH rats also had massive increase in Bacteroides spp., Fusobacterium spp., E. coli, Clostridium spp., Providencia spp., Prevotella interrmedia, and P. gingivalis while remarkable drop in Bifidobacteria spp. and Lactobacillus spp. Co-treatment with citicoline alone and with Lactobacillus improve histopathological NASH outcomes and reversed all of these molecular pathological alterations linked to NASH via upregulating the expression of Nrf2/HO-1 and downregulating TLR4/NF-kB signaling pathways. These results suggest that citicoline and lactobacillus may represent new hepatoprotective strategies against NASH progression. [ABSTRACT FROM AUTHOR]

Copyright of Infection is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Infection is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Inbred mouse strains KK.Cg-a/a and KK.Cg-Ay/a known as genetic models of type 2 diabetes mellitus significantly surpassed the control strain C57BL/6J in the body weight, relative weight of extractable fat, and basal blood glucose levels. Real-timePCR of fecal samples from KK.Cg-a/a and KK.Cg-Ay/a mice revealed dysbiosis typical of type 2 diabetes mellitus in humans and animals. Long-term intragastric administration of a suspension of Hafnia alvei bacteria had no effect on the above morphometric and biochemical parameters. At the same time, recovery of the Bacteroides spp. population in KK.Cg-Ay/a mice and a decrease in the number of Bifidobacterium spp. in KK.Cg-a/a mice were observed. The possibility of therapeutic use of the probiotic based on H. alvei is discussed. [ABSTRACT FROM AUTHOR]

Copyright of Infection is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Investigations into the mechanisms of antibiotic resistance gene transfer utilized by Bacteroides species have led to a greater understanding of how bacteria transfer antibiotic resistance genes, and what environmental stimuli promote such horizontal transfer events. Although Bacteroides spp. harbor a variety of transmissible elements that are involved in the dissemination of antibiotic resistance genes, it is one particular class of elements, the conjugative transposons, that are responsible for most of the resistance gene transfer in Bacteroides. The potential for Bacteroides conjugative transposons to transfer antibiotic resistance genes extends beyond those genes carried by the conjugative transposon itself, because Bacteroides conjugative transposons are able to mobilize coresident plasmids in trans and in cis, and also stimulate the excision and transfer of unlinked integrated elements called mobilizable transposons. These characteristics o f conjugative transposons alone have significant implications for the ecology and spread of antibiotic resistance genes, and in terms of biotechnology. A novel feature of the most widespread family of Bacteroides conjugative transposons, the CTnDOT/ERL family, is that their transfer is stimulated 100- to 1000-fold by low concentrations of tetracycline. This is significant because the use of antibiotics not only selects for resistant Bacteroides strains, but also stimulates their transfer. Other Bacteroides conjugative transposons do not require any induction to stimulate transfer, and hence appear to transfer constitutively. The constitutively transferring elements characterized so far appear to have a broader host range than the CTnDOT/ERL family of conjugative transposons, and the prevalence of these elements is on the increase. Since these constitutively transferring elements do not require induction by antibiotics to stimulate transfer, they have the potential to become as perva sive as the CTnDOT/ERL family of conjugative transposons. [ABSTRACT FROM AUTHOR]

Background: The quinolones developed over the past few years have enhanced in vitro activity and a broader spectrum of antimicrobial activity compared to many other antimicrobial agents including the older quinolones. The present study focuses on the effect of clinafloxacin, a member of the new broad-spectrum quinolone class of antibiotics, on the normal intestinal microflora. Subjects and Methods: A total of 12 healthy volunteers received clinafloxacin orally, 200 mg twice daily for 7 days. Fecal specimens were collected at defined intervals before, during and after the administration in order to study the effect of clinafloxacin on the intestinal microflora and to correlate this effect with fecal clinafloxacin concentrations. Intestinal microorganisms isolated before, during and 2 weeks after clinafloxacin administration were tested for their suseptibility to clinafloxacin. Results: Oral administration of clinafloxacin resulted in high drug levels in feces (mean value 176.2 mg/kg on day 7) and pronounced ecological disturbances. The aerobic microflora was eradicated in ii of the 12 subjects and the anaerobic microflora was strongly suppressed during administration. There was a significant emergence of clinafloxacin-resistant Bacteroides spp. strains (MIC ≥ 4 mg/ml) during administration. The elevated MIC values still remained 2 weeks after discontinuation of the antibiotic (p < 0.001). Conclusion: The emergence of clinafloxacin-resistant Bacteroides spp. demonstrates the necessity of restricting prescription for particular indications in order to preserve the efficacy of the highly active broad-spectrum quinolones. [ABSTRACT FROM AUTHOR]

Purpose : Chronic granulomatous disorder (CGD) is a primary immunodeficiency which is frequently complicated by inflammatory colitis and is associated with systemic inflammation. Herein, we aimed to investigate the role of the microbiome in the pathogenesis of colitis and systemic inflammation. Methods: We performed 16S rDNA sequencing on mucosal biopsy samples from each segment of 10 CGD patients' colons and conducted compositional and functional pathway prediction analyses. Results: The microbiota in samples from colitis patients demonstrated reduced taxonomic alpha-diversity compared to unaffected patients, even in apparently normal bowel segments. Functional pathway richness was similar between the colitic and non-colitic mucosa, although metabolic pathways involved in butyrate biosynthesis or utilization were enriched in patients with colitis and correlated positively with fecal calprotectin levels. One patient with very severe colitis was dominated by Enterococcus spp., while among other patients Bacteroides spp. abundance correlated with colitis severity measured by fecal calprotectin and an endoscopic severity score. In contrast, Blautia abundance is associated with low severity scores and mucosal health. Several taxa and functional pathways correlated with concentrations of inflammatory cytokines in blood but not with colitis severity. Notably, dividing patients into "high" and "low" systemic inflammation groups demonstrated clearer separation than on the basis of colitis status in beta-diversity analyses. Conclusion: The microbiome is abnormal in CGD-associated colitis and altered functional characteristics probably contribute to pathogenesis. Furthermore, the relationship between the mucosal microbiome and systemic inflammation, independent of colitis status, implies that the microbiome in CGD can influence the inflammatory phenotype of the condition. [ABSTRACT FROM AUTHOR]

Objective: To determine whether there is an association between the inflammatory potential of the diet, measured by the dietary inflammatory index (DII®), and the composition of intestinal microbiota in adults with functional constipation (FC). Methods: A cross-sectional study was carried out with 68 adults with FC. Energy-adjusted DII (E-DII) was calculated from data obtained from food surveys, serum inflammation markers were measured and the composition of the intestinal microbiota was evaluated using the 16S rRNA gene sequencing method. Participants were assigned into two groups: anti-inflammatory diet (AD: E-DII < 0) and pro-inflammatory diet (PD: E-DII ≥ 0). Associations of E-DII scores with microbial diversity and composition were examined using differences between the E-DII groups and linear and hierarchical regression. Results: E- DII was inversely correlated with relative abundance of Hungatella spp. and Bacteroides fragilis and positively correlated with Bacteroides thetaiotaomicron and Bacteroides caccae (p < 0.05). B. fragilis was positively correlated with IL-10. The AD group had higher relative abundances for the genus Blautia and Hungatella, lower abundances of Bacteroides thetaiotamicron and Bacteroides spp. (p < 0.05), as well as higher frequency of evacuation (p = 0.02) and lower use of laxatives (p = 0.05). The AD group showed a reduction in the abundance of Desulfovibrio spp. and Butyrivibrio, Butyrivibrio crossotus, Bacteroides clarus, Bacteroides coprophilus and Bacteroides intestinalis (all p < 0.05). The greater abundance of Bacteroides clarus increased the individual's chance of performing a manual evacuation maneuver. Conclusion: Therefore, the results of this study demonstrated that the inflammatory potential of the diet is associated with the gut microbiota in individuals with FC. [ABSTRACT FROM AUTHOR]

The infant gut microbiome contains a portion of bacteria that originate from the maternal gut. In the infant gut these bacteria encounter a new metabolic environment that differs from the adult gut, consequently requiring adjustments in their activities. We used pilot community RNA sequencing data (metatranscriptomes) from ten mother-infant dyads participating in the NiPPeR Study to characterize bacterial gene expression shifts following mother-to-infant transmission. Maternally-derived bacterial strains exhibited large scale gene expression shifts following the transmission to the infant gut, with 12,564 activated and 14,844 deactivated gene families. The implicated genes were most numerous and the magnitude shifts greatest in Bacteroides spp. This pilot study demonstrates environment-dependent, strain-specific shifts in gut bacteria function and underscores the importance of metatranscriptomic analysis in microbiome studies. [ABSTRACT FROM AUTHOR]

The early-life modifications of intestinal microbiota may impact children's subsequent emotional and cognitive development. Studies show that some bacteria species in gut microbiota, and the lack of others, may play a key role in autism spectrum disorders (ASD) development. Fecal samples were obtained from three groups of children: 16 healthy, 24 with allergies (ALG), and 33 with ASD (probiotics and non-probiotics users). The analysis was carried out according to the KyberKompakt Pro protocol. We observed a significantly higher level of Klebsiella spp. in the healthy children from the non-probiotics group, considering three groups. In the same group, Bifidobacterium spp. the level was lower in ASD compared to neurotypical individuals. In healthy children who did not use probiotics, strong positive correlations were observed in E. coli and Enterococcus spp. and Bacteroides and Klebsiella spp., and a negative correlation for Akkermansia muciniphila with both Klebsiella spp. and Bacteroides spp. In the ASD group who take probiotics, a strongly negative correlation was observed in Lactobacillus spp., and both Faecalibacterium prausnitzii and Akkermansia muciniphila levels. In the ALG group, the strongest, negative correlation was found between Enterococcus spp. and Lactobacillus spp. as in Akkermansia muciniphila and Bifidobacterium spp. The simple commercial test revealed minor differences in the composition of intestinal microorganisms between children with autism spectrum disorders and neurotypical peers. [ABSTRACT FROM AUTHOR]

A total of 978 strains of Bacteroides and Fusobacterium were tested for beta-lactamase production by a disk test (Cefinase) and a microtiter nitrocefin assay. In 83 % of strains both tests were positive and in 14.8 % both were negative. In 1.7 % of strains the disk test was positive and the microtiter test negative, and in 0.4 % the disk test negative but the microtiter test positive. The disk test was less discriminatory in detecting amoxicillin-resistant strains. The microtiter test was less sensitive than the disk test, but more discriminatory if results were read within 1 h for Fusobacterium spp., within 8 h for the Bacteroides fragilis group, and within 2 h for other Bacteroides spp. Neither test should be used clinically at present. [ABSTRACT FROM AUTHOR]

Bacteremia poses great risk for morbidity and mortality for immunocompromised cancer patients. Although the presence of bacteria within solid tumors is gaining greater attention, few studies have analyzed species of bacteria in the blood and their effect on cancer clinical outcomes. Using the Kraken 2 taxonomic profiling tool, we classified bacteria present in blood and primary tumors of cervical cancer and melanoma cases. The Cancer Genome Atlas (TCGA) melanoma blood exome files with Pseudomonas species were found to represent a worse disease-free survival (DFS) probability, while a worse overall survival (OS) result was evidenced for both the TCGA and Moffitt Cancer Center melanoma datasets. Cervical cancer cases with reads representing the Bradyrhizobium genus and Bradyrhizobium sp. BTAi1 found in blood and tumor exome files were found to have lower DFS. Additionally, reduced DFS and OS were observed for cervical cancer cases positive for Bacteroides species including Bacteroides fragilis. This study provides novel evidence and a novel approach for indicating that bacteria in blood is associated with cancer recurrence. These findings may guide the development of more efficient prognostic and screening tools related to bacterial blood infections of melanoma and cervical cancer patients. [ABSTRACT FROM AUTHOR]

We aimed to describe the microbiology of parapharyngeal abscess (PPA) and point out the likely pathogens using the following principles to suggest pathogenic significance: (1) frequent recovery, (2) abundant growth, (3) growth in relative abundance to other microorganisms, (4) percentage of the isolates recovered in both absolute and relative abundance, (5) more frequent recovery in PPA pus compared with tonsillar surface and tissue. Comprehensive bacterial cultures were performed on specimens obtained from adult patients (n = 60) with surgically verified PPA, who were prospectively enrolled at five Danish ear-nose-throat departments. The prevalent isolates (in PPA pus) were unspecified anaerobes (73%), non-hemolytic streptococci (67%), Streptococcus anginosus group (SAG) (40%), Corynebacterium spp. (25%), Neisseria spp. (23%), Fusobacterium spp. (22%), Fusobacterium necrophorum (17%), Prevotella spp. (12%), and Streptococcus pyogenes (10%). The bacteria most frequently isolated in heavy (maximum) growth were unspecified anaerobes (60%), SAG (40%), F. necrophorum (23%), and Prevotella spp. (17%). The predominant microorganisms (those found in highest relative abundance) were unspecified anaerobes (53%), SAG (28%), non-hemolytic streptococci (25%), F. necrophorum (15%), S. pyogenes (10%), and Prevotella spp. (10%). Four potential pathogens were found in both heavy growth and highest relative abundance in at least 50% of cases: F. necrophorum, Prevotella spp., SAG, and S. pyogenes. SAG, Prevotella spp., F. necrophorum, S. pyogenes, and Bacteroides spp. were recovered with the same or higher frequency from PPA pus compared with tonsillar tissue and surface. Our findings suggest that SAG, F. necrophorum, Prevotella, and S. pyogenes are significant pathogens in PPA development. [ABSTRACT FROM AUTHOR]

In the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both of Sardinian origin. Fecal bacterial composition of 46 OB patients (BMI = 36.6 ± 6.0; F/M = 40/6) was analyzed and compared to that of 46 NW subjects (BMI = 21.6 ± 2.1; F/M = 41/5), matched for sex, age and smoking status, by using 16S rRNA gene sequencing on MiSeq Illumina platform. The gut microbial community of OB patients exhibited a significant decrease in the relative abundance of several Bacteroidetes taxa (i.e. Flavobacteriaceae, Porphyromonadaceae, Sphingobacteriaceae, Flavobacterium, Rikenella spp., Pedobacter spp., Parabacteroides spp., Bacteroides spp.) when compared to NW; instead, several Firmicutes taxa were significantly increased in the same subjects (Lachnospiraceae, Gemellaceae, Paenibacillaceae, Streptococcaceae, Thermicanaceae, Gemella, Mitsuokella, Streptococcus, Acidaminococcus spp., Eubacterium spp., Ruminococcus spp., Megamonas spp., Streptococcus, Thermicanus, Megasphaera spp. and Veillonella spp.). Correlation analysis indicated that body fatness and waist circumference negatively correlated with Bacteroidetes taxa, while Firmicutes taxa positively correlated with body fat and negatively with muscle mass and/or physical activity level. Furthermore, the relative abundance of several bacterial taxa belonging to Enterobacteriaceae family, known to exhibit endotoxic activity, was increased in the OB group compared to NW. The results extend our knowledge on the GM profiles in Italian OB, identifying novel taxa linking obesity and intestine. [ABSTRACT FROM AUTHOR]

Purpose: Inulin is a soluble dietary fiber that has been implicated in regulating the intestinal health. Here, we describe a synergetic response of intestinal microbiota and epithelial functions to increased intake of inulin in a porcine model. Methods: Twenty growing-pigs were randomly allocated to two groups (n = 10) and fed with a basal diet (BD) or BD containing 0.5% inulin (INU) for 21 days. Results: We show that INU supplementation not only elevated villus height and the abundance of zonula occludens-1 (ZO-1), but also increased acetate and butyrate concentrations in cecum (P < 0.05). Moreover, INU decreased IL-6 and TNFα secretion, and reduced intestinal epithelial cell apoptosis in ileum and cecum (P < 0.05). Interestingly, we observed an elevated 16S rRNA gene copies in cecum after INU ingestion (P < 0.05). INU had no influence on overall diversity, but acutely altered the abundance of specific bacteria. INU decreased the abundance of phylum Proteobacteria in ileum, but increased the phylum Bacteroidetes in the ileum and cecum (P < 0.05). INU significantly elevated the Lactobacillus spp. and Bacteroides spp. in the ileum and cecum, respectively. Importantly, INU elevated the expression levels of GPR43, GLP-2, and ZO-1, but decreased the expression levels of histone deacetylase 1 (HDAC1) and TNFα in the ileum and cecum mucosa (P < 0.05). Moreover, INU also elevated the expression levels of GPR109A and angiopoietin-4 (ANG-4) in the cecum mucosa (P < 0.05). Conclusions: This study indicated how the intestinal microbiome and epithelium adapt to inulin ingestion, and furthered our understanding of the mechanisms behind the dietary fiber-modulated intestinal microbiota and health. [ABSTRACT FROM AUTHOR]

A variety of algorithms, forms and other clinical aids that relate to articles that appeared in the June 2011 issue of "Journal of Infection & Chemotherapy" are presented.

In order to describe the normal bacterial flora in vaginas of Criollo Limonero cows, 51 healthy multiparous cows, at least 90-day postpartum, were selected. Duplicated swabs ( N = 102) were taken from the vaginal fornix of cows to perform aerobic and anaerobic cultures as well as conventional biochemical tests. Out of 102 swabs, bacterial growth was obtained in 55 (53.9%) while the remaining 47 (46.1%) did not exhibited any bacterial growth. Of the 55 bacterial growths, 23 (41.8%) were aerobic whereas 32 (58.1%) were anaerobic. Likewise, 29 (52.72%) of bacterial growths were pure and 26 (47.27%) were mixed. Under both aerobic and anaerobic conditions, Gram positive bacteria were predominant (81.82% and 73.08%, respectively) over Gram negative bacteria (18.18% and 26.92%, respectively). Isolated bacteria were Arcanobacterium pyogenes (22.92%), Staphylococcus aureus (15.63%), Staphylococcus coagulase negative (17.71%), Erysipelothrix rhusiopathiae (6.25%), Bacteroides spp . (13.54%), and Peptostreptococcus spp . (7.29%). In conclusion, normal vaginal bacterial flora of Criollo Limonero cows was predominantly Gram positive and included A. pyogenes, S. aureus, coagulase negative Staphylococcus, E. rhusiopathiae, Bacteroides spp ., and Peptostreptococcus spp . In Criollo Limonero cattle, adaptive aspects such as development of humoral and physical mechanisms for defense, and bacterial adaptation to host deserve research attention. [ABSTRACT FROM AUTHOR]

Background and Objective: Ginseng is usually consumed as a dietary supplement for health care in the normal state or prescribed as a herbal medicine in pathologic conditions. Although metabolic studies of ginseng are commonly performed on healthy organisms, the metabolic characteristics in pathologic organisms remain unexplored. This study aimed to uncover the difference in intestinal metabolism of ginseng between normal and cyclophosphamide-induced immunosuppressed rats and further discuss the potential mechanisms involved. Methods: Twelve Sprague-Dawley rats (6–8 weeks old) were randomly divided into two groups: the normal group (NG) and immunosuppressed group (ISG). Rats in the NG and ISG groups were intraperitoneally administered normal saline and cyclophosphamide injections (40 mg/kg) on the 1st, 2nd, 3rd and 10th days; on the 12th day, all rats were intragastrically administered ginseng water extract (900 mg/kg). The difference in intestinal metabolism of ginseng was compared using an ultra-high-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry-based metabolomics approach, and the diversities of gut microbiota were analyzed by 16S rRNA gene sequencing between the two groups. Results: The intestinal metabolomic characteristics of ginseng were significantly different between the normal and immunosuppressed rats, with the ginsenoside F2 (F2), 20S-ginsenoside Rg3 (20(S)-Rg3), pseudo-ginsenoside Rt5 (Pseudo-Rt5), ginsenoside Rd (Rd), ginsenoside Rh1 (Rh1), 20S-ginsenoside Rg1 (20(S)-Rg1), ginsenoside compound K (CK), ginsenoside Rg2 (Rg2) and 20S-panaxatriol (S-PPT) more abundant in immunosuppressed ones (P < 0.05). Additionally, the composition of gut microbiota was remarkably altered in the two groups, with some specific bacterial communities such as Bacteroides spp., Eubacterium spp. and Lachnospiraceae_UCG-010 spp. increased and Bifidobacterium spp. decreased in immunosuppressed rats compared with normal ones. Conclusion: The intestinal metabolism of ginseng in immunosuppressed rats was significantly different from that in normal ones, which might be partly attributed to the changes in the intensity of specific gut bacteria. The outcomes of this study could provide scientific data for rationalization of ginseng use as both a dietary supplement and herbal medicine. [ABSTRACT FROM AUTHOR]

Purpose: Intraabdominal abscess (IAA) is a feared complication after laparoscopic appendectomy (LA) for complicated appendicitis. Benefits of obtaining intraoperative culture swabs (ICS) still remain controversial. We aimed to determine whether ICS modify the rate and management of IAA after LA for complicated appendicitis. Methods: A consecutive series of patients who underwent LA for complicated appendicitis from 2008 to 2018 were included. The cohort was divided into two groups: group 1 (G1), with ICS, and group 2 (G2), without ICS. Demographics, operative variables, pathogen isolation, antibiotic sensitivity, and postoperative outcomes were analyzed. Results: A total of 1639 LA were performed in the study period. Of these, 270 (16.5%) were complicated appendicitis; 90 (33%) belonged to G1 and 180 (67%) to G2. In G1, a higher proportion of patients had generalized peritonitis (G1, 63.3%; G2, 35%; p < 0.01). Seventy-two (80%) patients had positive cultures in G1. The most frequently isolated bacteria were E. coli (66.7%), Bacteroides spp. (34.7%), and Streptococcus spp. (19.4%). In 26 (36%) patients, the initial empiric antibiotic course was modified due to bacterial resistance. The rate of IAA was higher in patients with ICS (G1, 21.1%; G2, 9.4%; p = 0.01). IAA was treated similarly in both groups. A different type of bacteria was isolated in 7 (53.8%) patients with new culture swabs. Conclusions: Obtaining ICS in LA for complicated appendicitis with further antibiotic adjustment to the initial pathogen did not lower the incidence of postoperative IAA and did not modify the treatment needed for this complication. [ABSTRACT FROM AUTHOR]

Purpose: Wheat bran fibre has a beneficial effect on gastrointestinal function, but evidence for wheat germ is scarce. Accordingly, we evaluated the effects of daily intake of wheat germ on gastrointestinal discomfort and gut microbiota by adding wheat germ to refined (white) wheat bread, the most consumed bread type. We hypothesised that an improvement in the composition of refined bread could beneficially affect intestinal health without compromising consumers' acceptance. Methods: Fifty-five healthy adults were recruited for a randomised, double-blind, crossover, controlled trial comprising two 4-week intervention periods separated by a 5-week washout stage. During the first 4-week period, one group consumed wheat bread enriched with 6 g of wheat germ and the control group consumed non-enriched wheat bread. Results: Wheat germ-enriched bread was well-appreciated and the number of participants that demonstrated minimal gastrointestinal improvements after wheat-germ intake was higher than in the control arm. Importantly, intake of wheat germ-enriched bread decreased the perceived gastrointestinal discomfort-related quality of life (subscale worries and concerns) over refined white bread. The improvements in the gastrointestinal function were accompanied by favourable changes in gut microbiota, increasing the number of Bacteroides spp. and Bifidobacterium spp. Conclusions: Adding wheat germ to industrially made white bread without altering sensory properties may promote a healthy gut bacterial microbiota and the gastrointestinal health. [ABSTRACT FROM AUTHOR]

Clostridioides difficile infection (CDI) is one of the most common causes of nosocomial diarrhea in developed countries and the main cause in healthcare settings. This case–control study was designed to evaluate the composition of the gut microbiota dominant bacterial groups in patients with CDI compared to the healthy control subjects. A total of 100 adult subjects involving 50 inpatients with CDI and 50 healthy persons were enrolled in the study. C. difficile isolates were characterized according to the anaerobic culture and presence of toxin genes with multiplex PCR. An ecological analysis was performed real-time quantitative PCR for bacterial elements. The abundances of Enterococcus spp., Lactobacillus spp., Escherichia coli, C. difficile, and Akkermansia muciniphila were higher in group CDI compared with group HC (P < 0.05). The abundances of Bacteroides spp., Bifidobacterium spp., and Faecalibacterium prausnitzii were lower in group CDI than in group HC (P < 0.05). No significant difference was observed in the copy number of Prevotella genus between the CDI and HC subjects (P-value = 0.087). We observed that economic status and income levels were reduced at patients with CDI, however, there was no significant difference between CDI and HC group results and other variables, such as age, BMI, and educational level. These findings showed a reduction in butyrate-producing bacteria and increase in lactic acid-producing bacteria was seen in CDI status. Overrepresentation of Akkermansia may be a predictive marker for the development of nosocomial diarrhea can result in a worse CDI prognosis. [ABSTRACT FROM AUTHOR]

Aims: Gut microbiota significantly impacts human health and is influenced by dietary changes. We evaluated the effects of diets naturally rich in polyphenols (PP) and/or long-chain n-3 polyunsaturated fatty acids (LCn3) on microbiota composition in an ancillary analysis of a randomized controlled trial in individuals at high cardiometabolic risk. Methods: Seventy-eight individuals with high waist circumference and at least one additional component of the metabolic syndrome were randomized to an isoenergetic 8-week diet: (a) low LCn3 and PP; (b) high LCn3; (c) high PP; or (d) high LCn3 and PP. Microbiota analysis was performed on feces collected before and after the intervention. DGGE analysis of the predominant bacteria, Eubacterium rectale and Blautia coccoides group (Lachnospiraceae, EREC), Clostridium leptum (Ruminococcaceae, CLEPT), Bacteroides spp., Bifidobacteria, and Lactobacillus group was performed. A quantitative real-time PCR was performed for the same group, additionally including Atopobium cluster (Coriobatteriaceae). Before and after the intervention, participants underwent a 75 g OGTT and a high-fat test meal to evaluate glucose and lipid response. Results: Adherence to the four diets was optimal. PP significantly increased microbial diversity (p = 0.006) and CLEPT (p = 0.015), while it reduced EREC (p = 0.044). LCn3 significantly increased the numbers of Bifidobacteria (p = 0.041). Changes in CLEPT numbers correlated with changes in early insulin secretion (r = 0.263, p = 0.030). Changes in Atopobium numbers correlated with postprandial triglycerides in plasma (r = 0.266, p = 0.026) and large VLDL (r = 0.313, p = 0.009), and cholesterol in large VLDL (r = 0.319, p = 0.008). Conclusions: Diets naturally rich in PP or LCn3 influenced gut microbiota composition in individuals at high cardiometabolic risk. These modifications were associated with changes in glucose/lipid metabolism. [ABSTRACT FROM AUTHOR]

Gut microbes are linked to host metabolism, but specific mechanisms remain to be uncovered. Ceramides, a type of sphingolipid (SL), have been implicated in the development of a range of metabolic disorders from insulin resistance (IR) to hepatic steatosis. SLs are obtained from the diet and generated by de novo synthesis in mammalian tissues. Another potential, but unexplored, source of mammalian SLs is production by Bacteroidetes, the dominant phylum of the gut microbiome. Genomes of Bacteroides spp. and their relatives encode serine palmitoyltransfease (SPT), allowing them to produce SLs. Here, we explore the contribution of SL-production by gut Bacteroides to host SL homeostasis. In human cell culture, bacterial SLs are processed by host SL-metabolic pathways. In mouse models, Bacteroides- derived lipids transfer to host epithelial tissue and the hepatic portal vein. Administration of B. thetaiotaomicron to mice, but not an SPT-deficient strain, reduces de novo SL production and increases liver ceramides. These results indicate that gut-derived bacterial SLs affect host lipid metabolism. [ABSTRACT FROM AUTHOR]

Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp. [ABSTRACT FROM AUTHOR]

A total of 43 patients, 11 males and 32 females, with paronychia of the fingernails were examined for the presence of Candida spp. The yeast species isolated were identified using standard laboratory methods, including germ-tube production, morphology on rice agar with Tween 80, and mainly fermentation and assimilation of saccharides. In the male group, two Candida species were detected: C. albicans as the dominant species in 9 patients and C. parapsilosis in 2 cases. Similarly, C. albicans was the prevalent species also in females ( n = 17); other Candida species detected were C. parapsilosis ( n = 7), C. tropicalis (5) and C. krusei (3). In addition to the genus Candida, the following anaerobic and aerobic microorganisms were isolated from patients of both groups: Fusobacterium spp., Bacteroides spp., Staphylococcus aureus, α-hemolytic streptococci, group A β-hemolytic streptococci, Klebsiella pneumoniae, Neisseria spp. and Pseudomonas aeruginosa. [ABSTRACT FROM AUTHOR]

Microbial granules were grown in a column-type sequential aerobic sludge blanket reactor inoculated with activated sludge flocs taken from a wastewater treatment plant and containing a medium with glucose as the main carbon source. The reactor selected for granules that could settle rapidly by employing a short settling time of 2 min. Matured granules with diameters between 2 and 3 mm were examined for anaerobic bacteria as their presence can signal the onset of diffusion limitation problems that can potentially diminish granule stability due to the bacterial production of fermentation gases and organic acids under anaerobic conditions. To detect the anaerobes in the granules, clones were constructed from 16S rRNA PCR amplicons. Two sequence types associated with a strict anaerobe Bacteroides spp. were identified from these clones. Fluorescence in situ hybridization (FISH) followed by confocal laser scanning microscopy (CLSM) demonstrated that cells of Bacteroides spp. were concentrated at a depth of approximately 800 mm below the surface of the granule. Cell enumeration using flow cytometry showed that the percentage of labeled cells of Bacteroides spp. compared to total bacterial cells in the granules was 0.56%. This is the first study to use a suite of culture-independent techniques to report the presence of a defined species of anaerobic bacteria in aerobically grown microbial granules. [ABSTRACT FROM AUTHOR]

Human gut Bacteroides and Parabacteroides species play crucial roles in human health and are known for their capacity to utilize diverse polysaccharides. Understanding how these bacteria utilize medicinal polysaccharides is foundational for developing polysaccharides-based prebiotics and drugs. Here, we systematically mapped the utilization profiles of 20 different medicinal polysaccharides by 28 human gut Bacteroides and Parabacteroides species. The growth profiles exhibited substantial variation across different bacterial species and medicinal polysaccharides. Ginseng polysaccharides promoted the growth of multiple Bacteroides and Parabacteroides species; in contrast, Dendrobium polysaccharides selectively promoted the growth of Bacteroides uniformis. This distinct utilization profile was associated with genomic variation in carbohydrate-active enzymes, rather than monosaccharides composition variation among medicinal polysaccharides. Through comparative transcriptomics and genetical manipulation, we validated that the polysaccharide utilization locus PUL34_Bu enabled Bacteroides uniformis to utilize Dendrobium polysaccharides (i.e. glucomannan). In addition, we found that the GH26 enzyme in PUL34_Bu allowed Bacteroides uniformis to utilize multiple plant-derived mannan. Overall, our results revealed the selective utilization of medicinal polysaccharide by Bacteroides and Parabacteroides species and provided insights into the use of polysaccharides in engineering the human gut microbiome. Here, the authors characterize the utilization of 20 medicinal polysaccharides by 28 human gut Bacteroides and Parabacteroides species, revealing substantial variability in bacterial growth responses, which they link to genomic differences in carbohydrate-active enzymes. [ABSTRACT FROM AUTHOR]

Maintaining a diverse and balanced sow milk microbiome is essential to piglet development. Thus, this study aimed to examine the effects of probiotic Bacillus licheniformis supplementation on the microbiome composition of sow colostrum and milk, and to review associated health findings in piglets. B. licheniformis DSMZ 28710 was supplemented at 10 g/day as feed additive before predicted farrowing until weaning by top dressing. Colostrum and milk samples were collected for metagenomic DNA extraction, 16s rRNA sequencing, and bioinformatics analyses for bacterial microbiota diversity. Results indicated that the supplementation increased the abundances of beneficial bacteria, such as Lactobacillus, Pediococcus, Bacteroides, and Bifidobacterium, while decreasing the abundances of pathogenic bacteria, such as Staphylococcus aureus, Enterobacteriaceae, and Campylobacter in the colostrum. The supplementation increased diversity while maintaining richness and evenness. Moreover, the rise in predicted microbial community metabolic function in membrane transport pathways provides crucial evidence showing that the supplementation is potentially beneficial to piglets, as these pathways are important for providing nutrients and immunity to offspring. This research highlights the importance of microbiome composition in sow milk and the potential of B. licheniformis supplementation as a means to improve piglet health and development. [ABSTRACT FROM AUTHOR]

Paramount to human health, symbiotic bacteria in the gastrointestinal tract rely on the breakdown of complex polysaccharides to thrive in this sugar-deprived environment. Gut Bacteroides are metabolic generalists and deploy dozens of polysaccharide utilization loci (PULs) to forage diverse dietary and host-derived glycans. The expression of the multi-protein PUL complexes is tightly regulated at the transcriptional level. However, how PULs are orchestrated at translational level in response to the fluctuating levels of their cognate substrates is unknown. Here, we identify the RNA-binding protein RbpB and a family of noncoding RNAs as key players in post-transcriptional PUL regulation. We demonstrate that RbpB interacts with numerous cellular transcripts, including a paralogous noncoding RNA family comprised of 14 members, the FopS (family of paralogous sRNAs). Through a series of in-vitro and in-vivo assays, we reveal that FopS sRNAs repress the translation of SusC-like glycan transporters when substrates are limited—an effect antagonized by RbpB. Ablation of RbpB in Bacteroides thetaiotaomicron compromises colonization in the mouse gut in a diet-dependent manner. Together, this study adds to our understanding of RNA-coordinated metabolic control as an important factor contributing to the in-vivo fitness of predominant microbiota species in dynamic nutrient landscapes. Gut Bacteroides deploy several polysaccharide utilization loci (PULs) to forage diverse dietary and host-derived glycans. Here, the authors identify the RNA-binding protein RbpB and a family of noncoding RNAs as key players in post-transcriptional PUL regulation, further showing that ablation of RbpB in Bacteroides thetaiotaomicron compromises colonization in the mouse gut in a diet-dependent manner. [ABSTRACT FROM AUTHOR]

Decomposition of submerged plants releases organic matter, nitrogen, and phosphorus into water bodies, generating an important impact on the aquatic ecosystem. This study explored the influence of growth substrate with different compositions on the decomposition process of eelgrass (Vallisneria spinulosa Yan, V. spinulosa Yan). The sediment + iron–carbon fillers system exhibited significantly lower concentrations of total nitrogen (TN) and total phosphorus (TP) in the overlying water than other systems, with the maximum values of 5.68 and 7.05 mg/L, respectively. The addition of ceramic and calcium nitrate promoted the formation of HCl-extracted phosphorus (HCl–P) in the sediment, while the addition of iron–carbon fillers increased the content of NaOH-extracted phosphorus (NaOH–P). Three-dimensional fluorescence spectroscopy of dissolved organic matter (DOM) in overlying water showed that different substrate compositions did not significantly affect the compositions of organic matter released during the decomposition of V. spinulosa Yan. The microbial community and abundance in each experimental group changed significantly before and after the decomposition of V. spinulosa Yan. The sediment + iron–carbon fillers system showed significantly higher abundance of microbial community than other systems, with the enrichment of functional bacteria related to denitrification and sulfate reduction. In contrast, the sediment + calcium nitrate system exhibited a smaller change of microbial community abundance, with the enrichment of aerobic denitrifying bacteria. In this paper, it was found that the sediment + iron–carbon group had a good adsorption effect on nitrogen and phosphorus released during the decomposition process of V. spinulosa Yan, and had a good effect on water purification as the growth substrate of submerged plants. [ABSTRACT FROM AUTHOR]

Since therapeutic options are limited the utilization of prebiotics is suggested to prevent food allergies (FAs). Using an experimental peach allergy model we explored the effect of dietary fiber pectin, a high-methoxyl heteropolysaccharide, on the manifestation of FA. CBA/J mice were sensitized, subsequently orally boosted and provoked with peach peel extract. For dietary intervention, mice were fed a pectin containing diet before (primary-preventive) or after (secondary-preventive) sensitization. Non-treated allergic and sham-treated mice were fed a diet containing 20% cellulose. Fecal microbiota, humoral and intestinal immune cell responses were analyzed. Pectin remarkably affected the gut microbiota composition and diversity, promoting mainly the growth of Bacteroides. The frequency of mast cells, macrophages, and CD3+T cells in the lamina propria of the small intestine was reduced, whereas the frequency of B cells and CD4+T cell subpopulation was enhanced. Pectin intervention in the primary-preventive stetting significantly triggered serum IgA levels, whereas production of IgE and mMCPT-1 was reduced. Remarkably, in both settings peach allergen-specific IgG1/IgG2a ratio and specific IgE were significantly reduced to baseline. The data suggest, that dietary supplementation of pectin in both intervention approaches can diminish inflammatory responses and signs of allergic immune responses, accompanied by alteration of the gut microbiota composition. [ABSTRACT FROM AUTHOR]

Colorectal cancer (CRC) is second most deadly and third most commonly diagnosed cancer in the world. CRC cases have been increasing lately with a shift to fast food diets, unhealthy lifestyles and other environmental conditions. The gut microbiota thriving on dietary fibres and worn off mucus layers plays a decisive role in the homeostasis of the gut. In dysbiosis, this consortium of commensal microbes is replaced by harmful microbes, rather the pathogens leading to catastrophic outcomes with respect to the individual's well-being, like chronic inflammation, interference in cellular mechanisms, promotion of tumour micro-environments, induction of prooncogenic immunity pathways, etc. A number of microorganisms are known to participate in tumorigenesis, working as 'driver' or 'passenger' bacteria with resultant oncogenic outcomes. Organisms like Bacillus fragilis, Porphyromonas gingivalis, Fusobacterium nucleatum, Streptococcus gallolyticus, collagenolytic Enterococcus faecalis, Peptostreptococcus anaerobius, E. coli and others have the ability to induce proinflammatory genes and precancerous precursors modulating the immune system and the stromal cells to support the growth of tumour. Mechanisms of these organisms participating in tumour growth, promotion and metastasis are mentioned and briefed about in this review. In most cases, the presence of these microbes is observed only after the tumour has already set in or in pre-cancerous stages, generally making the revival of the commensal population difficult to recolonise. Every individual has unique resident microbial footprint, showing virulence in one and not in another. Hence attempts should be made to maintain a diet rich in dietary fibres with a healthy lifestyle to avoid dysbiosis and further complications. [ABSTRACT FROM AUTHOR]