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and , cohabitants in the intestinal mucosa, are considered members of a healthy microbiota and reduction of both species occurs in several intestinal disorders, including inflammatory bowel disease. Little is known however about a possible link between the reduction in quantity of these species, and in which circumstances this may occur. This study aims to determine the abundances and co-occurrence of the two species in order to elucidate conditions that may compromise their presence in the gut. Loads of , total and its two phylogroup (16S rRNA gene copies) were determined by quantitative polymerase chain reaction in colonic biopsies from 17 healthy controls (H), 23 patients with ulcerative colitis (UC), 31 patients with Crohn's disease (CD), 3 with irritable bowel syndrome (IBS) and 3 with colorectal cancer (CRC). Data were normalized to total bacterial 16S rRNA gene copies in the same sample. Prevalence, relative abundances and correlation analyses were performed according to type of disease and considering relevant clinical characteristics of patients such as IBD location, age of disease onset, CD behavior, current medication and activity status. Co-occurrence of both species was found in 29% of H, 65% of UC and 29% of CD. Lower levels of total and phylogroups were found in subjects with CD, compared with H subjects ( ≤ 0.044). In contrast, no differences were found with the regard to abundance across different disease states, but CD patients with disease onset below 16 years of age featured a marked depletion of this species. In CD patients, correlation between and total (ρ = 0.362, = 0.045) was observed, and particularly in those with non-stricturing, non-penetrating disease behavior and under moderate immunosuppressants therapy. Altogether, this study revealed that co-occurrence of both species differs between disease status. In addition, IBD patients featured a reduction of but similar loads of when compared to H subjects, with the exception of those with early onset CD. Depletion of in this subgroup of subjects suggests that it could be a potential biomarker to assist in pediatric CD diagnosis.

[This corrects the article DOI: 10.1371/journal.pone.0243158.].

Gut microbiota may be involved in the presence of irritable bowel syndrome (IBS)-like symptomatology in ulcerative colitis (UC) patients in remission. Bread is an important source of dietary fiber, and a potential prebiotic. To assess the effect of a bread baked using traditional elaboration, in comparison with using modern elaboration procedures, in changing the gut microbiota and relieving IBS-like symptoms in patients with quiescent ulcerative colitis. Thirty-one UC patients in remission with IBS-like symptoms were randomly assigned to a dietary intervention with 200 g/d of either treatment or control bread for 8 weeks. Clinical symptomatology was tested using questionnaires and inflammatory parameters. Changes in fecal microbiota composition were assessed by high-throughput sequencing of the 16S rRNA gene. A decrease in IBS-like symptomatology was observed after both the treatment and control bread interventions as reductions in IBS-Symptom Severity Score values ( p- value < 0.001) and presence of abdominal pain ( p- value < 0.001). The treatment bread suggestively reduced the Firmicutes/Bacteroidetes ratio ( p- value = 0.058). In addition, the Firmicutes/Bacteroidetes ratio seemed to be associated with improving IBS-like symptoms as suggested by a slight decrease in patient without abdominal pain ( p- value = 0.059). No statistically significant differential abundances were found at any taxonomic level. The intake of a bread baked using traditional elaboration decreased the Firmicutes/Bacteroidetes ratio, which seemed to be associated with improving IBS-like symptoms in quiescent ulcerative colitis patients. These findings suggest that the traditional bread elaboration has a potential prebiotic effect improving gut health (ClinicalTrials.gov ID number of study: NCT05656391).

BackgroundMany studies have shown the importance of the relationship between intestinal microbiota and health in recent years. This has led to the development of different microbiota tests, but still, there is a need to provide tests that determine dysbiosis. In this line, it was developed a microbial panel to summarize the gut microbiota state and identify dysbiosis, consisting of 15 key microbial markers representing the human intestinal microbiota.This work aimed to clinically validate the robustness of the microbial markers panel by comparing its outcomes with clinical parameters and the dysbiosis index use.MethodsThere were recruited 154 subjects undergoing the microbiota panel analysis. Clinical data and diagnosis of the enrolled subjects were recorded. Total DNA was extracted, and the abundance of the microbial markers was analysed by qPCR. Statistical analysis was performed using RStudio.ResultsA MANOVA analysis determined no significant differences between genders when the microbial abundance that composes the panel is analysed. In addition, no significant differences were observed according to the patient‘s age classification. The microbial panel showed significant differences (p-value 0.017) according to the type of stool (diarrhoea, constipation, or mixed), observing an inverse behaviour in A.muciniphila and M.smithii. The dysbiosis index was divided into healthy, temporary, and dysbiotic. Significant differences were observed when comparing the abundance of the markers to the dysbiosis index (p-value <0.001), showing how when the dysbiosis index is healthy; there is minimal variation in the microbial markers panel; when it is temporary, the variation increases, and when it is dysbiotic, the general dysbiosis is evident.ConclusionsThe clinical validation of the panel of microbial markers demonstrated to be a good indicator of the general state of the intestinal microbiota and to overcome 2 factors: gender and age, and to differentiate 2 dysbiosis degrees.This test could be a potential first step towards the quantification of the intestinal microbiota not only with application to digestive diseases but for all conditions that have already been shown to have dysbiosis.

The fecal immunochemical test (FIT) is the most widely used test for colorectal cancer (CRC) screening. RAID-CRC Screen is a new non-invasive test based on fecal bacterial markers, developed to complement FIT by increasing its specificity. The test was previously clinically evaluated in FIT-positive patients (>20 μg of hemoglobin/g of feces, “FIT20”), in which it reduced the proportion of false positive results by 16.3% while maintaining most of FIT20’s sensitivity. The aim of this study was to compare the sensitivity and specificity of a CRC screening program using RAID-CRC Screen in addition to FIT20 as a triage test in a European screening population undergoing screening colonoscopy with a CRC screening program with FIT20 alone in the same cohort. A cohort of 2481 subjects aged > 55 years from the German screening colonoscopy program was included. The colonoscopy findings were used as the gold standard in calculating the diagnostic capacity of the tests and included 15 CRC and 257 advanced neoplasia cases. RAID-CRC Screen added to FIT20 provided the same sensitivity as FIT20 alone (66.7%) in detecting CRC and a significantly higher specificity (97.0% vs. 96.1%, p<0.0001). The positive predictive value was 11.9% when using RAID-CRC Screen and 9.5% with FIT20 alone, and the negative predictive value was 99.8% in the two scenarios. For advanced neoplasia detection, the use of RAID-CRC Screen yielded significantly lower sensitivity than with FIT20 alone (17.5% vs. 21.8%, p = 0.0009), and the overall specificity was significantly higher when using RAID-CRC Screen compared with FIT20 alone (98.2% vs. 97.8%, p = 0.0039). Our findings confirm the results obtained in previous clinical studies in a CRC screening setting, showing the potential of RAID-CRC Screen to increase the overall specificity of FIT-based screening.

Escherichia coli, particularly the adherent-invasive E. coli (AIEC) pathovar, has been increasingly implicated in the ethiopathogenesis of Crohn's disease (CD). We describe the richness, abundance, diversity, and pathogenic features of E. coli and AIEC strains that colonize the intestinal mucosa.MethodsApproximately 100 E. coli colonies per biopsy from 20 CD patients (18 biopsies from colon and 23 from ileum) and 28 healthy controls (C) (25, colon; 27, ileum) were isolated. Repetitive extragenic palindrome-polymerase chain reaction (Rep-PCR) and pulsed field gel electrophoresis (PFGE) were used to analyze the clonality of isolates. For AIEC identification, adhesion and invasion assays were performed over Intestine-407 cells, and the capacity to survive and replicate intracellularly was determined over macrophages J774. The serotypes, phylotypes, and genotypes (19 virulence genes) of strains were also investigated.ResultsMucosa-associated E. coli richness (E. coli subtypes/patient: C = 2.0 ± 1.0; CD = 2.1 ± 1.3) and diversity (Shannon Index: H'C: 2.1 ± 0.6; H'CD: 2.5 ± 0.8) were similar between CD and C, but higher E. coli counts were characteristic of CD patients (P = 0.010), particularly those with Crohn's ileitis (P = 0.001). Host-specific pulsotypes shared virulence features of ExPEC at similar frequencies between CD and C, except for iucD, which was more prevalent in E. coli from controls (C: 75%, CD: 40%, P = 0.027). In contrast, greater AIEC prevalence (% subjects with AIEC: CD = 51.9%; C = 16.7%; P = 0.003), abundance (% AIEC/E. coli: CD = 3.8 ± 5.0%; C = 1.5 ± 3.8%; P = 0.039), and richness (number of AIEC subtypes: CD = 0.8 ± 1.4; C = 0.2 ± 0.4; P = 0.015) of E. coli strains belonging to the AIEC pathovar was observed for CD patients. AIEC subtypes showed a high variability of seropathotypes and pulsotypes, although the B2 phylogroup was the most prevalent (AIEC: 64%, non-AIEC: 38%, P = 0.044).ConclusionsNew data about ecological parameters of AIEC reinforces the implication of AIEC in CD.

Guidelines recommend routine screening for colorectal cancer (CRC) in asymptomatic adults starting at age 50. The most extensively used noninvasive test for CRC screening is the fecal immunochemical test (FIT), which has an overall sensitivity for CRC of approximately 61.0%-91.0%, which drops to 27.0%-67.0% for advanced adenomas. These figures contain a high false-positive rate and a low positive predictive value. This work aimed to develop a new, noninvasive CRC screening tool based on fecal bacterial markers capable of decreasing FIT false-positive rates in a FIT-positive population. We defined a fecal bacterial signature ( RAID-CRC Screen ) in a proof-of-concept with 172 FIT-positive individuals and validated the obtained results on an external cohort of 327 FIT-positive subjects. All study participants had joined the national CRC screening program. In the clinical validation of RAID-CRC Screen , a sensitivity of 83.9% and a specificity of 16.3% were obtained for the detection of advanced neoplasm lesions (advanced adenomas and/or CRC). FIT 20 μg/g produced 184 false-positive results. Using RAID-CRC Screen , this value was reduced to 154, thus reducing the false-positive rate by 16.3%. The RAID-CRC Screen test could be implemented in CRC screening programs to allow a significant reduction in the number of colonoscopies performed unnecessarily for FIT-positive participants of CRC screening programs.

Background Crohn's disease (CD) is a high morbidity chronic inflammatory disorder of unknown aetiology. Adherent-invasive Escherichia coli (AIEC) has been recently implicated in the origin and perpetuation of CD. Because bacterial biofilms in the gut mucosa are suspected to play a role in CD and biofilm formation is a feature of certain pathogenic E. coli strains, we compared the biofilm formation capacity of 27 AIEC and 38 non-AIEC strains isolated from the intestinal mucosa. Biofilm formation capacity was then contrasted with the AIEC phenotype, the serotype, the phylotype, and the presence of virulence genes. Results Specific biofilm formation (SBF) indices were higher amongst AIEC than non-AIEC strains (P = 0.012). In addition, 65.4% of moderate to strong biofilms producers were AIEC, whereas 74.4% of weak biofilm producers were non-AIEC (P = 0.002). These data indicate that AIEC strains were more efficient biofilm producers than non-AIEC strains. Moreover, adhesion (P = 0.009) and invasion (P = 0.003) indices correlated positively with higher SBF indices. Additionally, motility (100%, P < 0.001), H1 type flagellin (53.8%, P < 0.001), serogroups O83 (19.2%, P = 0.008) and O22 (26.9%, P = 0.001), the presence of virulence genes such as sfa/focDE (38.5%, P = 0.003) and ibeA (26.9%, P = 0.017), and B2 phylotype (80.8%, P < 0.001) were frequent characteristics amongst biofilm producers. Conclusion The principal contribution of the present work is the finding that biofilm formation capacity is a novel, complementary pathogenic feature of the recently described AIEC pathovar. Characterization of AIEC specific genetic determinants, and the regulatory pathways, involved in biofilm formation will likely bring new insights into AIEC pathogenesis.

BackgroundBacteria might play a role in the pathogenesis of Crohn's disease (CD), and patients harbor a different type and density of gut microbiota compared with normal healthy subjects. Thus, the aim of this study was to compare the microbiota adhered to the mucosa of CD patients with that of healthy subjects.MethodsPolymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene fragments was used to identify the dominant bacterial species present in fresh biopsy samples obtained from the mucosa of 15 healthy and 19 CD subjects. Two patients suffering from ulcerative colitis and 1 suffering from ischemic colitis also were included.ResultsIndividuals were clustered in 2 groups according to their molecular fingerprint, which differentiated the majority of CD specimens (88.2%) from the majority of healthy/ulcerative colitis/ischemic colitis specimens (82.3%). In addition, the patient-to-patient variability in microbiota was greater within the CD cluster than in the healthy/ulcerative colitis cluster (P = 0.000). One hundred forty-one sequences were obtained from the PCR-DGGE bands that were grouped into 58 different phylotypes, 8 of which were novel. BLAST analysis revealed that 74.5% of the sequences were similar to those of bacteria that have never been cultivated. In CD samples, prevalence values for Clostridium spp Ruminococcus torques and Escherichia coli were significantly higher, whereas Faecalibacterium was more frequently found in healthy specimens. Opportunistic pathogenic γ-proteobacteria were found occasionally, only in CD mucosal microbiota.ConclusionsMicrobiota attached to the ileocolonic mucosa of CD patients is distinguishable from that of healthy subjects. We postulate that individuals who are predisposed to CD are less able to regulate the microbial makeup of their intestines, which leads to an unstable microbial population.

The measures adopted to control the spread of the COVID-19 pandemic in several countries included mobility and social restrictions that produced an immediate impact on the lifestyle of their inhabitants. We assessed the association between the consequences of these measures and depressive symptomatology using a population-based sample of 692 individuals aged 18 or over from an ongoing study in the province of Girona (Catalonia, Spain). Participants responded to a telephone-based survey that included questions related to the consequences of confinement and the Patient Health Questionnaire-9 (PHQ-9) was used to assess depressive symptomatology. Multivariate logistic and linear regressions were used to identify which changes in lifestyle resulting from confinement were independently associated with a possible depression episode and depressive symptomatology. The prevalence of a possible depressive episode during the confinement was 12.7% (95% CI = 10.3–15.4). An adverse work situation, expected economic distress, self-reported worsening of the mental health and of the dietary pattern, and worries about a relative's potential infection were variables related to an increased risk of having a possible depressive episode. The changes in lifestyle accounted for 32% of the variance of the PHQ-9 score. The findings indicate an association of the job situation, the expected negative economic consequences, the perceived worsening of health and habits, and the worries about COVID-19 infection with depressive symptomatology during the confinement. •The prevalence of depressive episode during the confinement among individuals aged 18 years or over was 12.7%.•Work status, expected economic distress, health worsening, and reduction of activities were related to depressive symptoms.•Affective symptoms were related to the length of confinement and somatic symptoms with physical activity restrictions.