Cytometric fingerprints of gut microbiota predict Crohn’s disease state

Variations in the gut microbiome have been associated with changes in health state such as Crohn’s disease. Most surveys characterize the microbiome through analysis of the 16S rRNA gene. An alternative technology that can be used is flow cytometry. In this report we analyzed a disease cohort that has been characterized by both technologies. Changes in microbial community structure are reflected in both types of data. We demonstrate that cytometric fingerprints can be used as a diagnostic tool in order to classify samples according to Crohn’s disease state. These results highlight the potential of flow cytometry to perform rapid diagnostics of microbiome-associated diseases.

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OC-051 Siblings Of Crohn’s Disease Patients Exhibit A Biologically Relevant Dysbiosis In The Mucosal Microbial Community: A 16s Rrna Gene Pyrosequencing Study: Abstract OC-051 Table 1

Gut ◽

10.1136/gutjnl-2014-307263.51 ◽

2014 ◽

Vol 63 (Suppl 1) ◽

pp. A25.1-A25 ◽

Cited By ~ 2

Author(s):

C Hedin ◽

C van der Gast ◽

GB Rogers ◽

S McCartney ◽

AJ Stagg ◽

...

Keyword(s):

Crohn’S Disease ◽

Microbial Community ◽

Crohn's Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

Rrna Gene ◽

Biologically Relevant ◽

16S Rrna Gene Pyrosequencing

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Azithromycin and the microbiota of cystic fibrosis sputum

BMC Microbiology ◽

10.1186/s12866-021-02159-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Nicole Acosta ◽

Christina S. Thornton ◽

Michael G. Surette ◽

Ranjani Somayaji ◽

Laura Rossi ◽

...

Keyword(s):

Cystic Fibrosis ◽

Community Structure ◽

Microbial Community ◽

Lung Function ◽

Rrna Gene ◽

Lung Function Decline ◽

Disease Pathogenesis ◽

Cystic Fibrosis Sputum ◽

Clustering Effect ◽

The 16S Rrna Gene

Abstract Background Azithromycin is commonly prescribed drug for individuals with cystic fibrosis (CF), with demonstrated benefits in reducing lung function decline, exacerbation occurrence and improving nutrition. As azithromycin has antimicrobial activity against components of the uncultured microbiome and increasingly the CF microbiome is implicated in disease pathogenesis – we postulated azithromycin may act through its manipulation. Herein we sought to determine if the CF microbiome changed following azithromycin use and if clinical benefit observed during azithromycin use associated with baseline community structure. Results Drawing from a prospectively collected biobank we identified patients with sputum samples prior to, during and after initiating azithromycin and determined the composition of the CF microbial community by sequencing the V3-V4 region of the 16S rRNA gene. We categorized patients as responders if their rate of lung function decline improved after azithromycin initiation. Thirty-eight adults comprised our cohort, nine who had not utilized azithromycin in at least 3 years, and 29 who were completely naïve. We did not observe a major impact in the microbial community structure of CF sputum in the 2 years following azithromycin usage in either alpha or beta-diversity metrics. Seventeen patients (45%) were classified as Responders – demonstrating reduced lung function decline after azithromycin. Responders who were naïve to azithromycin had a modest clustering effect distinguishing them from those who were non-Responders, and had communities enriched with several organisms including Stenotrophomonas, but not Pseudomonas. Conclusions Azithromycin treatment did not associate with subsequent large changes in the CF microbiome structure. However, we found that baseline community structure associated with subsequent azithromycin response in CF adults.

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Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

Animal Microbiome ◽

10.1186/s42523-021-00074-8 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Sesilje Weiss ◽

David Taggart ◽

Ian Smith ◽

Kristofer M. Helgen ◽

Raphael Eisenhofer

Keyword(s):

Microbial Community ◽

Reproductive Cycle ◽

Tammar Wallaby ◽

The Body ◽

Rrna Gene ◽

Microbial Composition ◽

Birth Canal ◽

Gram Positive Bacteria ◽

Rigorous Framework ◽

The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

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Novel strain-level resolution of Crohn’s disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing

The ISME Journal ◽

10.1038/s41396-021-00991-1 ◽

2021 ◽

Author(s):

J. J. Teh ◽

E. M. Berendsen ◽

E. C. Hoedt ◽

S. Kang ◽

J. Zhang ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Ex Vivo ◽

Taxonomic Composition ◽

Strain Level ◽

Patient Specific ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Functional Characterisation ◽

Bacterial Lineages

AbstractThe mucosa-associated microbiota is widely recognized as a potential trigger for Crohn’s disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative Crohn’s disease patients. The 16 S rRNA gene amplicon profiles showed these cultures provide a representative and holistic representation of the mucosa-associated microbiota, and MC-MGS produced both high quality metagenome-assembled genomes of recovered novel bacterial lineages. The MC-MGS approach also produced a strain-level resolution of key Enterobacteriacea and their associated virulence factors and revealed that urease activity underpins a key and diverse metabolic guild in these communities, which was confirmed by culture-based studies with axenic cultures. Collectively, these findings using MC-MGS show that the Crohn’s disease mucosa-associated microbiota possesses taxonomic and functional attributes that are highly individualistic, borne at least in part by novel bacterial lineages not readily isolated or characterised from stool samples using current sequencing approaches.

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Funding the New Biologics – CCOHTA Report on the Cost Effectiveness of Infliximab for Crohn’s Disease: Pearls and Pitfalls

Canadian Journal of Gastroenterology ◽

10.1155/2002/859517 ◽

2002 ◽

Vol 16 (12) ◽

pp. 877-879 ◽

Cited By ~ 1

Author(s):

John K Marshall

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Economic Analysis ◽

Safety Data ◽

Cost Utility ◽

Sensitivity Analyses ◽

State Transitions ◽

Health State ◽

Life Years ◽

The Cost

The Canadian Coordinating Office for Health Technology Assessment (CCOHTA) published an economic analysis, using a Markov model, of infliximab therapy for Crohn’s disease that is refractory to other treatments. This was the first fully published economic analysis that addresses this treatment option. Health state transitions were based on data from Olmsted County, Minnesota, health state resource profiles were created using expert opinion and a number of assumptions were made when designing the model. The analysis was rigorous, the best available efficacy and safety data were used, state-of-the art sensitivity analyses were undertaken and an ‘acceptability curve‘ was constructed. The model found that infliximab was effective in increasing quality-adjusted life years when offered in a variety of protocols, but it was associated with high incremental cost utility ratios compared with usual care. The results should be interpreted, however, in view of a number of limitations. The time horizon for the analysis was short (one year), because of a lack of longer-term efficacy data, and might have led to an underestimation of the benefits from averting surgery. Because the analysis was performed from the perspective of a Canadian provincial ministry of health, only direct medical costs were considered. Patients with active Crohn’s disease are likely to incur significant indirect costs, which could be mitigated by this medication. The analysis should be updated as new data become available. Moreover, small changes in the cost of the medication could make the treatment cost effective, according to this model. Economic analyses, such as the one undertaken by the CCOHTA, cannot by themselves solve dilemmas in the allocation of limited health care resources, and other considerations must be included when formulating policy. This is especially important for patients with severe Crohn’s disease, who have significant disability and for whom few therapeutic options exist.

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Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa006 ◽

2020 ◽

Vol 96 (2) ◽

Cited By ~ 4

Author(s):

Kärt Kanger ◽

Nigel G H Guilford ◽

HyunWoo Lee ◽

Camilla L Nesbø ◽

Jaak Truu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Solid State ◽

Food Waste ◽

Microbial Community Structure ◽

Microbial Community Composition ◽

Microbial Community Analysis ◽

Waste Paper ◽

Rrna Gene ◽

Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

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Decreased Enteric Bacterial Composition and Diversity in South American Crohn’s Disease Vary With the Choice of Treatment Strategy and Time Since Diagnosis

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjz189 ◽

2019 ◽

Vol 14 (6) ◽

pp. 791-800

Author(s):

Angélica Cruz-Lebrón ◽

Leticia D’argenio Garcia ◽

Aarthi Talla ◽

Samira Joussef-Piña ◽

Miguel E Quiñones-Mateu ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Gut Microbiota ◽

Bacterial Diversity ◽

Relative Abundance ◽

Treatment Strategy ◽

Chronic Inflammatory Disease ◽

Rrna Gene ◽

Faecal Calprotectin ◽

Time Since Diagnosis

Abstract Background and Aims The symptomology of Crohn’s disease [CD], a chronic inflammatory disease of the digestive tract, correlates poorly with clinical, endoscopic or immunological assessments of disease severity. The prevalence of CD in South America is rising, reflecting changes in socio-economic stability. Many treatment options are available to CD patients, including biological agents and corticosteroids, each of which offers variable efficacy attributed to host genetics and environmental factors associated with alterations in the gut microbiota. Methods Based on 16S rRNA gene sequencing and taxonomic differences, we compared the faecal microbial population of Brazilian patients with CD treated with corticosteroid or anti-tumour necrosis factor [anti-TNF] immunotherapy. Faecal calprotectin and plasma sCD14 levels were quantified as markers for local and systemic inflammation, respectively. Results Anti-TNF treatment led to an increased relative abundance of Proteobacteria and a decreased level of Bacteroidetes. In contrast, corticoid treatment was associated with an increase in the relative abundance of Actinobacteria, which has been linked to inflammation in CD. Disruption of the faecal microbiota was related to decreased bacterial diversity and composition. Moreover, the choice of clinical regimen and time since diagnosis modulate the character of the resulting dysbiosis. Conclusions Enteric microbial populations in CD patients who have been treated are modulated by disease pathogenesis, local inflammatory microenvironment and treatment strategy. The dysbiosis that remains after anti-TNF treatment due to decreased bacterial diversity and composition abates restoration of the microbiota to a healthy state, suggesting that the identification and development of new clinical treatments for CD must include their capacity to normalize the gut microbiota.

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Faecal Microbiota Dynamics and their Relation to Disease Course in Crohn’s Disease

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjz049 ◽

2019 ◽

Vol 13 (10) ◽

pp. 1273-1282 ◽

Cited By ~ 4

Author(s):

Gianluca Galazzo ◽

Danyta I Tedjo ◽

Dion S J Wintjens ◽

Paul H M Savelkoul ◽

Ad A M Masclee ◽

...

Keyword(s):

Crohn’S Disease ◽

Community Structure ◽

Microbial Community ◽

Disease Activity ◽

Microbial Community Structure ◽

Disease Course ◽

Microbiota Composition ◽

Faecal Microbiota ◽

Over Time

Abstract Background Microbial shifts have been associated with disease activity in Crohn’s disease [CD], but findings on specific taxa are inconsistent. This may be due to differences in applied methods and cross-sectional study designs. We prospectively examined the faecal microbiota in adult CD patients with changing or stable disease course over time. Methods Faeces were collected at two time-points from 15 healthy control individuals [HCs], 35 CD patients who were in remission and who maintained remission [RRs], and 22 CD patients during remission and also during subsequent exacerbation [RAs]. The microbial composition was assessed by 16S rRNA [V4] gene sequencing. Results Compared with HCs, patients with CD had a lower microbial richness [p = 0.0002] and diversity [p = 0.005]. Moreover, the microbial community structure of a subset of patients, clustered apart from HCs, was characterized by low microbial diversity and Faecalibacterium abundance. Patients within this cluster did not differ with respect to long-term disease course compared with patients with a ‘healthy-appearing’ microbiota. Over time, microbial richness and diversity did not change in RR versus RA patients. Although the microbial community structure of both RR and RA patients was less stable over time compared with that of HCs, no differences were observed between the patient groups [p = 0.17]; nor was the stability impacted by Montreal classification, medication use, or surgery. Conclusion The altered microbiota composition and stability in CD was neither associated with disease activity nor long-term disease course, questioning its involvement in the development of an exacerbation. The aberrant microbiota composition in a subset of CD patients warrants further exploration of a more microbiota-driven etiology in this group.

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