Quantitative characterization of Clostridioides difficile population in the gut microbiome of patients with C. difficile infection and their association with clinical factors

Abstract Objective was to analyse bacterial composition and abundance of Clostridioides difficile in gut microbiome of patients with C. difficile infection (CDI) in association with clinical characteristics. Whole metagenome sequencing of gut microbiome of 26 CDI patients was performed, and the relative abundance of C. difficile and its toxin genes was measured. Clinical characteristics of the patients were obtained through medical records. A strong correlation between the abundance of C. difficile and tcdB genes in CDI patients was found. The relative abundance of C. difficile in the gut microbiome ranged from undetectable to 2.8% (median 0.089). Patients with fever exhibited low abundance of C. difficile in their gut, and patients with fewer C. difficile organisms required long-term anti-CDI treatment. Abundance of Bifidobacterium and Bacteroides negatively correlated with that of C. difficile at the genus level. CDI patients were clustered using the bacterial composition of the gut: one with high population of Enterococcus (cluster 1, n = 12) and another of Bacteroides or Lactobacillus (cluster 2, n = 14). Cluster1 showed significantly lower bacterial diversity and clinical cure at the end of treatment. Additionally, patients with CDI exhibited increased ARGs; notably, blaTEM, blaSHV and blaCTX-M were enriched. C. difficile existed in variable proportion of the gut microbiome in CDI patients. CDI patients with Enterococcus-rich microbiome in the gut had lower bacterial diversity and poorer clinical cure.

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Faecal bacterial composition in horses with and without free faecal liquid: a case control study

Scientific Reports ◽

10.1038/s41598-021-83897-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Katrin M. Lindroth ◽

Johan Dicksved ◽

Erik Pelve ◽

Viveca Båverud ◽

Cecilia E. Müller

Keyword(s):

Relative Abundance ◽

Case Control Study ◽

Sampling Period ◽

Rrna Gene ◽

Bacterial Composition ◽

Clostridioides Difficile ◽

Liquid Phases ◽

And Control ◽

The 16S Rrna Gene ◽

Control Study

AbstractFree faecal liquid (FFL) is a condition in horses which manifests as differential defecation of solid and liquid phases of faeces. The etiology of FFL is currently unknown, but deviances in the hindgut microbiota has been suggested to be of importance. The present study aimed to compare the faecal bacterial composition of farm-matched horses with (case, n = 50) and without (control, n = 50) FFL. Samples were collected at three different occasions. The V3 and V4 regions of the 16S rRNA gene were amplified and sequenced using Illumina sequencing. Also, samples were cultivated for detection of Clostridioides difficile and Clostridium perfringens. Analysis revealed similar faecal bacterial composition between case and control horses, but an effect of sampling period (p = 0.0001). Within sampling periods, 14 genera were present in higher or lower proportions in case compared to control horses in at least one sampling period. Compared to controls, case horses had higher relative abundance of Alloprevotella (adjusted p < 0.04) and lower relative abundance of Bacillus spp. (adjusted p < 0.03) in at least two sampling periods. All horses tested negative for C. difficile and C. perfringens by culture of faeces. Further studies are required to establish the clinical relevance of specific bacterial taxa in FFL.

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Clinical Characteristics and Fecal Microbiome in Recurrent Versus Nonrecurrent Clostridioides difficile Infection

Antimicrobial Stewardship & Healthcare Epidemiology ◽

10.1017/ash.2021.77 ◽

2021 ◽

Vol 1 (S1) ◽

pp. s41-s42

Author(s):

Swapnil Lanjewar ◽

Ashley Kates ◽

Lauren Watson ◽

Nasia Safdar

Keyword(s):

Gut Microbiome ◽

Clinical Characteristics ◽

Academic Medical Center ◽

Tertiary Care ◽

Ribosomal Database Project ◽

Data Set ◽

Β Diversity ◽

Clostridioides Difficile ◽

Increased Risk ◽

Multiple Recurrences

Background: Up to 30% of patients with Clostridioides difficile infection (CDI) develop recurrent infection, which is associated with a 33% increased risk of mortality at 180 days. The gut microbiome plays a key role in initial and recurrent episodes of CDI. We examined the clinical characteristics and gut microbial diversity in patients with recurrent (rCDI) versus nonrecurrent CDI at a tertiary-care academic medical center. Methods: Stool samples were collected from 113 patients diagnosed with CDI between 2018 and 2019. Clinical and demographic data were extracted from the electronic medical record (Table 1), and 16S rRNA sequencing of the v4 region was carried out on the Illumina MiSeq using 2×250 paired-end reads. Sequences were binned into operational taxonomic units (OTUs) using mothur and were classified to the genus level whenever possible using the ribosomal database project data set version 16. Alpha diversity was calculated using the Shannon diversity index. Β diversity was calculated using the Bray-Curtis dissimilarity matrix. Differential abundance testing was done using DESeq to assess taxonomic differences between groups. A P value of .05 was used to assess significance. Results: In total, 55 patients had rCDI (prior positive C. difficile polymerase chain reaction in last 7–365 days) and 58 had nonrecurrent CDI (Table 1). Patients with rCDI had a higher frequency of organ transplant and comorbidity. No differences in α not β diversity were observed between groups. Also, 4 OTUs were more abundant in those with rCDI: Ruminococcus (n = 2), Odoribacter, and Lactobacillus. Patients with rCDI had microbiomes with greater proportions of Bacteroidetes (27% of OTUs) compared to the nonrecurrent group (18%) as well as fewer OTUs belonging to the Firmicutes phyla compared to the nonrecurrent patients (56% vs 59%). Among the rCDI patients, those experiencing 2 or more recurrences had greater abundances of Bacteroides and Ruminococcus, while those experiencing only 1 recurrence had significantly greater abundances of Akkermensia, Ruminococcus, Streptococcus, Roseburia, Clostridium IV, and Collinsella compared to those with only 1 recurrence (Table 2). Conclusions: Patients with rCDI had a more impaired microbiome than those with initial CDI. Ruminococcus OTUs have been previously indicated as a risk factor for recurrence and treatment failure, and they were significantly more abundant in those with rCDI and among those with multiple recurrences. The greatest differences in the microbiome were observed between those with 1 recurrence compared to those with multiple recurrences. Interventions for gut microbiome restoration should focus particularly on those with recurrent CDI.Funding: NoDisclosures: None

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Gut microbiome and its cofactors are linked to lipoprotein distribution profiles

10.1101/2021.09.01.458531 ◽

2021 ◽

Author(s):

Josue Castro Mejia ◽

Bekzod Khakimov ◽

Mads Lind ◽

Eva Garne ◽

Petronela Paulova ◽

...

Keyword(s):

Relative Abundance ◽

Gut Microbiome ◽

Short Chain Fatty Acids ◽

Future Research ◽

Lipoprotein Subfractions ◽

Lipoprotein Subclasses ◽

Metagenome Sequencing ◽

Lipoprotein Distribution ◽

Host Characteristics

Increasing evidence indicates that the gut microbiome (GM) plays an important role in the etiology of dyslipidemia. To date, however, no in depth characterization of the associations between GM and its metabolic attributes with deep profiling of lipoproteins distributions (LPD) among healthy individuals has been conducted. To determine associations and contributions of GM composition and its cofactors with distribution profiles of lipoprotein subfractions, we studied blood plasma LPD, fecal short-chain fatty acids (SCFA) and GM of 262 healthy Danish subjects aged 19-89 years. Stratification of LPD segregated subjects into three clusters of profiles that reflected differences in the lipoprotein subclasses, corresponded well with limits of recommended levels of main lipoprotein fractions and were largely explained by host characteristics such as age and body mass index. Higher levels of HDL, particularly driven by large subfractions (HDL2a and HDL2b), were associated with a higher relative abundance of Ruminococcaceae and Christensenellaceae. Increasing levels of total cholesterol and LDL, which were primarily associated with large 1 and 2 subclasses, were positively associated with Lachnospiraceae and Coriobacteriaceae, and negatively with Bacteroidaceae and Bifidobacteriaceae. Metagenome sequencing showed a higher abundance of genes involved in the biosynthesis of multiple B-vitamins and SCFA metabolism among subjects with healthier LPD profiles. Metagenomic assembled genomes (MAGs) affiliated mainly to Eggerthellaceae and Clostridiales were identified as the contributors of these genes and whose relative abundance correlated positively with larger subfractions of HDL. The results of this study demonstrate that remarkable differences in composition and metabolic traits of the GM are associated with variations in LPD among healthy subjects. Findings from this study provide evidence for GM considerations in future research aiming to shade light on mechanisms of the GM - dyslipidemia axis.

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Weaning age and its effect on the development of the swine gut microbiome and resistome

10.1101/2021.05.20.444551 ◽

2021 ◽

Author(s):

Devin B Holman ◽

Katherine E Gzyl ◽

Kathy T Mou ◽

Heather K Allen

Keyword(s):

Relative Abundance ◽

Gut Microbiome ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Carbohydrate Active Enzymes ◽

Fecal Microbiome ◽

Shotgun Metagenomic Sequencing ◽

Swine Operations ◽

Weaning Age

Piglets are often weaned between 19 and 22 d of age in North America although in some swine operations this may occur at 14 d or less. Piglets are abruptly separated from their sow at weaning and are quickly transitioned from sow's milk to a plant-based diet. The effect of weaning age on the long-term development of the pig gut microbiome is largely unknown. In this study, pigs were weaned at either 14, 21, or 28 d of age and fecal samples collected 21 times from d 4 (neonatal) through to marketing at d 140. The fecal microbiome was characterized using 16S rRNA gene and shotgun metagenomic sequencing. The fecal microbiome of all piglets shifted significantly three to seven days post-weaning with an increase in microbial diversity. Several Prevotella spp. increased in relative abundance immediately after weaning as did butyrate-producing species such as Butyricicoccus porcorum, Faecalibacterium prausnitzii, and Megasphaera elsdenii. Within 7 days of weaning, the gut microbiome of pigs weaned at 21 and 28 days of age resembled that of pigs weaned at 14 d. Resistance genes to most antimicrobial classes decreased in relative abundance post-weaning with the exception of those conferring resistance to tetracyclines and macrolides-lincosamides-streptogramin B. The relative abundance of microbial carbohydrate-active enzymes (CAZymes) changed significantly in the post-weaning period with an enrichment of CAZymes involved in degradation of plant-derived polysaccharides. These results demonstrate that pigs tend to have a more similar microbiome as they age and that weaning age has only a temporary effect on the gut microbiome.

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Bacterial Diversity and Community in Response to Long-Term Nitrogen Fertilization Gradient in Citrus Orchard Soils

Diversity ◽

10.3390/d13070282 ◽

2021 ◽

Vol 13 (7) ◽

pp. 282

Author(s):

Yu Wan ◽

Wenjie Li ◽

Jie Wang ◽

Xiaojun Shi

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Relative Abundance ◽

Nitrogen Fertilizer ◽

Citrus Orchard ◽

Fertilizer Rate ◽

Nitrogen Fertilizer Rate ◽

Citrus Orchards ◽

Orchard Soils

Citrus orchards receive increasing amounts of nitrogen fertilizer for the purpose of optimal yields and good quality of citrus fruits. Although the effects of increased nitrogen fertilizer on citrus fruit trees have been reasonably well studied, few comparable studies have examined impacts on soil bacterial communities and diversity, even though they play critical roles in orchard ecosystem functioning. In our study, Illumina MiSeq sequencing was used to investigate bacterial community structure and diversity under 5-years long-term nitrogen fertilization gradients (N0, N1, N2, N3, N4, and N5) in citrus orchard soils. The sequencing result showed that nitrogen fertilizer addition increased bacterial diversity along the N0 to N3 gradient but decreased bacterial diversity along the N3 to N5 gradient. The increase in the nitrogen fertilizer rate altered bacterial community composition by increasing the relative abundance of Delta-proteobacteria, Nitrospirae, SBR1093, and Latescibacteria and decreasing the relative abundance of Alpha-proteobacteria. Finally, regression analysis revealed that bacterial diversity and the relative abundance of Nitrosomonadales, Rhodobiaceae, Gemmatimonas, and Variibacter exhibited a significant positive correlation with citrus yield. The study revealed that a reasonable nitrogen fertilizer rate applied to citrus orchards could improve bacterial community structure and diversity and increase citrus yield.

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Walnuts and Vegetable Oils Differentially Affect the Gut Microbiome and Associations with Cardiovascular Risk Factors (OR29-06-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz031.or29-06-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Cited By ~ 1

Author(s):

Alyssa Tindall ◽

Christopher McLimans ◽

Kristina Petersen ◽

Penny Kris-Etherton ◽

Regina Lamendella

Keyword(s):

Risk Factors ◽

Vegetable Oils ◽

Relative Abundance ◽

Gut Microbiome ◽

Saturated Fatty Acids ◽

Secondary Analysis ◽

Cvd Risk Factors ◽

Cvd Risk ◽

Bacterial Composition ◽

Linear Discriminant

Abstract Objectives To examine gut bacterial composition following a higher-saturated fatty acids (SFA) run-in, standard Western diet (SWD) and 3 study diets where SFA was replaced with: whole walnuts (WD); vegetable oils in a fatty acid matched diet devoid of walnuts (WFMD); vegetable oils in an oleic acid replaces α-linolenic acid (ALA) diet (ORAD) and devoid of walnuts. Correlations between the bacterial composition and cardiovascular disease (CVD) risk factors were also explored. Methods Adults at CVD risk (n = 42) were included in this secondary analysis of a randomized, crossover, controlled-feeding study that reported improvements in CVD risk factors. Only significantly changed risk factors were correlated with significantly enriched bacteria. Fecal collections followed a 2-week run-in diet and three 6-week diet periods. Linear discriminant analysis Effect Size plots were used to determine enriched taxa. Results Following the WD, Roseburia (mean relative abundance = 4.2%, LDA = 4, P = 0.0008), Eubacterium eligensgroup (1.4%, 4, 0.05), Lachnospiraceae UCG001 (1.2%, 3, 0.03), Lachnospiraceae UCG004 (1.0%, 3, 0.04) and Leuconostocaceae (0.03%, 3, 0.05) were abundant relative to the SWD. Relative to the SWD, Roseburia (mean relative abundance = 3.6%, LDA = 4, P = 0.02) and Eubacterium eligensgroup (1.5%, 3, 0.02) were enriched following the WFMD, and following the ORAD Clostridialesvadin BB60 (0.3%, 2, 0.04) was most abundant. Significant associations existed between enriched bacteria following the WD and CVD risk factors. Eubacterium eligens correlated with brachial (R = −0.5, P = 0.0009) and central mean arterial pressure (MAP; −0.5, 0.002), and central diastolic blood pressure (cDBP; −0.5, 0.0006). Lachnospiraceae correlated with brachial (R = −0.4, P = 0.02) and central MAP (−0.4, 0.02), cDBP (−0.3, 0.04), total cholesterol (TC; −0.4, 0.03), and non-HDL-C (−0.4, 0.02). Leuconostocaceae correlated with brachial (R = 0.3, P = 0.03) and central MAP (0.3, 0.03). Conclusions Similar eubiotic bacteria were enriched by the WD and WFMD suggesting ALA and linoleic acid affect the gut microbiome. Enrichment of Lachnospiraceae and associations with improved CVD risk factors suggests the microbiome contributes to the beneficial health effects of walnuts. Funding Sources The California Walnut Commission and National Center for Advancing Translational Sciences, NIH. Supporting Tables, Images and/or Graphs

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Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial

10.21203/rs.3.rs-39860/v2 ◽

2020 ◽

Author(s):

Suryang Kwak ◽

JooHee Choi ◽

Tiffany Hink ◽

Kimberly A. Reske ◽

Kenneth Blount ◽

...

Keyword(s):

Relative Abundance ◽

Gut Microbiome ◽

Post Treatment ◽

Patient Specific ◽

Controlled Clinical Trial ◽

Investigational Drug ◽

Metagenomic Sequencing ◽

Double Blind ◽

Significant Recovery ◽

Clostridioides Difficile

Abstract Background. Intestinal microbiota restoration can be achieved by complementing a subject’s perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic resistant genes (ARGs) and organisms (AROs). In this study, we investigated fecal specimens from a multicenter, randomized, double-blind, placebo-controlled phase 2b study of microbiota-based investigational drug RBX2660. Patients were administered either placebo, 1 dose of RBX2660 and 1 placebo, or 2 doses of RBX2660 via enema and longitudinally tracked for changes in their microbiome and antibiotic resistome.Results. All patients exhibited significant recovery of gut microbiome diversity and a decrease of ARG relative abundance during the first 7 days post-treatment. However, the microbiome and resistome shifts towards average configurations from unperturbed individuals were more significant and longer-lasting in RBX2660 recipients compared to placebo. We quantified microbiome and resistome modification by RBX2660 using a novel ‘transplantation index’ metric. We identified taxonomic and metabolic features distinguishing the baseline microbiome of non-transplanted patients and taxa specifically enriched during the process of transplantation. We elucidated the correlation between resistome and taxonomic transplantations and post-treatment dynamics of patient-specific and RBX2660-specific ARGs. Whole genome sequencing of AROs cultured from RBX2660 product and patient samples indicate ARO eradication in patients via RBX2660 administration, but also, to a lesser extent, introduction of RBX2660-derived AROs.Conclusions. Through shotgun metagenomic sequencing, we elucidated the effects of RBX2660 in the microbiome and resistome. Antibiotic discontinuation alone resulted in significant recovery of gut microbial diversity and reduced ARG relative abundance, but RBX2660 administration more rapidly and completely changed the composition of patients’ microbiome, resistome, and ARO colonization by transplanting RBX2660 microbiota into the recipients. Although ARGs and AROs were transmitted through RBX2660, the resistome post-RBX2660 more closely resembled that of the administered product—a proxy for the donor—than an antibiotic perturbed state.Trial registration: NCT02299570. Registered 19 November 2014, https://clinicaltrials.gov/ct2/show/NCT02299570

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