Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease

Ibrahim, Ahmad; Valles, Camille; Maatouk, Mohamad; Bittar, Fadi; Alou, Maryam Tidjani; Raoult, Didier

doi:10.1128/cmr.00140-21

Cited by 25 publications

(38 citation statements)

References 197 publications

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“…Diets that are imbalanced by being low in complex polysaccharides (and therefore, based on carbohydrates) and rich in protein intake can change the composition of the gut microbiota by decreasing the percentages of Bacteroidetes (B) over Firmicutes (F), leading to irregular saccharolytic fermentation [ 13 ]. This imbalance in the microbial ecosystem is called dysbiosis, defined by the altered representation of Phyla percentages [ 14 ]. Dysbiosis can lead to the numerical expansion of some/certain potentially pathogenic commensal bacterial species.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Gut Microbiota Composition in Type 2 Diabetes Patients: A Population-Based Study

Polidori¹,

Marullo²,

Ialongo

et al. 2022

IJERPH

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(1) Background: A clinical laboratory index to assess gut dysbiosis is the F/B ratio < 0.8. In fact, an elevated proportion of Firmicutes and a reduced population of Bacteroides in diabetes type 2 (T2D) subjects has been observed. This study aimed to detail the dysbiosis status in the Italian population, focusing on some pathogenic spectra (T2D) or metabolic disorders. (2) Material and methods: A quantity of 334 fecal samples was analyzed in order to perform genetic testing and sequencing. (3) Results: A trend in over imbalance was observed in the percentage of Proteobacteria (median value: 6.75%; interquartile range (IQR): 3.57–17.29%). A statistically significant association (χ2p = 0.033) was observed between type of dysbiosis and T2D, corresponding to an Odds Ratio (OR) of 1.86. It was noted that females with cystitis/candidiasis are significantly prevalent in T2D patients (p < 0.01; OR: 3.59; 95% CI: 1.43–8.99). Although, in non-diabetic males, a sugar craving is significantly associated with the rate of dysbiosis in non-diabetic males (p < 0.05; OR 1.07; 95% CI 1.00–1.16). (4) Conclusion: In T2D patients, the Bacteroidetes/Firmicutes ratio was biased in favor of Proteobacteria, to be expected due to the nutritional habits of the patients. Thus, T2D females had altered gut permeability favoring the development of infections in the vaginal tract.

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Section: Introductionmentioning

confidence: 99%

Characterization of Gut Microbiota Composition in Type 2 Diabetes Patients: A Population-Based Study

Polidori¹,

Marullo²,

Ialongo

et al. 2022

IJERPH

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“…This was supported by the sequencing results which con rmed that different species of Candidatus Saccharibacteria could be found. Indeed, studies have previously established that the same host can be host to different Candidatus Sacchairbacteria 10,14 .…”

Section: Discussionmentioning

confidence: 99%

“…Open reading frames (ORFs) were predicted using Prokka 41 for each of the genomes studied. In order to show the mosaicism of these two described genome, we constructed a rhizomal representation of each genome, as a previously described 10,42,43 . This representation shows the origin of each amino acid sequences and determine the possible lateral gene transfer between our CPR genomes and other microbes 43 .…”

Section: Genome Annotation and Genes Predictionmentioning

confidence: 99%

“…This is exempli ed by their small genome size (approximately 1 Mb) 3,7 and a reduction in their essential metabolic activity compared to the usual metabolic pathways of non-CPR bacteria 3 . Indeed, with few exceptions, the lack of metabolic pathways involved in amino and fatty acid biosynthesis was previously described 3,[8][9][10] . In addition, the lack of electron transport pathway complexes and an absence of ATP synthase compared to those of non-CPR bacteria were also reported 3,11 .…”

Section: Introductionmentioning

confidence: 99%

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Genomic description and prevalence of two new Candidatus Saccharibacteria species from the human gut in different samples and countries

Caputo

Anani

Ibrahim

et al. 2022

Preprint

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The candidate phyla radiation (CPR) has been described as an obligatory group of ultrasmall bacteria associated with host bacteria. They phylogenetically represent a subdivision of bacteria distinct from other living organisms. Using polyphasic approaches, we screened human faecal samples for the detection of Saccharibacteria. The new sequences obtained by sequencing were compared to the complete CPR genomes available to date. Then, we attempted a co-culture of CPR-bacteria and non-CPR bacteria from human faecal samples. We finally aimed to evaluate the prevalence and distribution of these Saccharibacteria sequences in human sources in 16S amplicon datasets. We were able to reconstitute two high-quality Saccharibacteria genomes named Minimicrobia massiliensis and Minimicrobia timonensis. We have established, for the first time in human digestive samples, the coculture of Candidatus Saccharibacteria with two different bacterial hosts. Finally, we showed that 12.8% (610/4,756) of samples sequenced in our laboratory were positive for operational taxonomic units (OTUs) assigned to M.massiliensis. and significantly enriched in human respiratory and oral microbiota. Here, we reported the first genomes and coculture of Saccharibacteria from human gut specimens. This study opens a new field, particularly in the study of the involvement of CPR in the human intestinal microbiota.

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“…Interest in human microbiome-associated Saccharibacteria, Gracilibacteria, and Absconditabacteria (hereafter referred to as SGA) has increased, in part due to their association with disease 1 . SGA are lineages within the Candidate Phyla Radiation (CPR), a monophyletic radiation within domain Bacteria, and are characterized in part by their consistently reduced genomes, small cell sizes, and limited metabolic capabilities 2 .…”

Section: Introductionmentioning

confidence: 99%

Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria

Liu

Jaffe

Chen

et al. 2022

Preprint

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Within human microbiomes, Gracilibacteria, Absconditabacteria, and Saccharibacteria, members of Candidate Phyla Radiation (CPR), are increasingly correlated with human oral health and disease. We sought phages that are capable of infecting these bacteria, as these may prove effective for phage therapies to control oral microbiome composition. To do this we analyzed spacer inventories from CRISPR-Cas systems that themselves could be used for phage editing. Absconditabacteria and Gracilibacteria recode the typical TGA stop codon to glycine and are infected by phages that share their host's alternate genetic code. Unexpectedly, however, other predicted phages of Gracilibacteria and Absconditabacteria do not use an alternative genetic code. Some of these phages are predicted to infect both alternatively coded CPR bacteria and the standard code host bacteria upon which the CPR bacteria depend. These phages rely on other stop codons, and thus should be capable of producing viable gene products in either bacterial host type. Interestingly, we predict that phages of Saccharibacteria can replicate in Actinobacteria, which are likely the Saccharibacteria hosts. Overall, this broad host range behavior may be advantageous for the production of CPR phage therapy agents, as non-CPR bacteria are easier to cultivate than CPR bacteria. Absconditabacteria and Gracilibacteria phages may have avoided acquisition of in-frame stop codons to increase the diversity of bacteria in which they can replicate.

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Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease

Cited by 25 publications

References 197 publications

Characterization of Gut Microbiota Composition in Type 2 Diabetes Patients: A Population-Based Study

Characterization of Gut Microbiota Composition in Type 2 Diabetes Patients: A Population-Based Study

Genomic description and prevalence of two new Candidatus Saccharibacteria species from the human gut in different samples and countries

Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria

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