Approximation of a Microbiome Composition Shift by a Change in a Single Balance Between Two Groups of Taxa

Odintsova, Vera; Klimenko, Natalia; Tyakht, Alexander

doi:10.1128/msystems.00155-22

Cited by 10 publications

(20 citation statements)

References 29 publications

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“…Overall, microbiome composition on the level of species was significantly associated with the sample type (paired PERMANOVA with correction on Shannon index, p = 0.0001, R 2 = 27%). A more detailed comparison of stool and biopsy using the nearest balance method [ 30 ] showed 20 species reproducibly associated with the stool samples, and 14 species—with biopsy ( Supplementary Table S1 ). The stool vs. biopsy distinction was emphasized by the absolute results of area under the curve analysis (average AUC on the test set across 500 iterations of cross-validation was equal to 1 ± 0).…”

Section: Resultsmentioning

confidence: 99%

“…Our study is the first one to statistically examine the links of pre-CRC microbiome composition with the lesion characteristics using a compositionality-aware approach (specifically, via our novel method—the nearest balance [ 30 ]). Compositional statistical algorithms provide more accurate results by accounting for the fact that the microbiome sequencing data inherently do not provide the absolute quantity of each taxon, but only their relative abundance (i.e., they are compositional).…”

Section: Discussionmentioning

confidence: 99%

“…Alpha diversity was compared using the Wilcoxon rank sum test. Relative abundance of individual taxa in stool and biopsy was performed at the level of species using the nearest balance [ 30 ] method according to the following mixed linear model: balance ~ sample_type + (1|patient_id) where balance is the sought nearest balance; sample_type—type of sample (stool/biopsy); patient_id—identifier of subject; (1|…)—random effect.…”

Section: Methodsmentioning

confidence: 99%

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Luminal and Tumor-Associated Gut Microbiome Features Linked to Precancerous Lesions Malignancy Risk: A Compositional Approach

Романов¹,

Karasev

Klimenko

et al. 2022

Cancers

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Colorectal cancer is the third most commonly diagnosed cancer worldwide. Human gut microbiome plays important roles in protecting against it, as well as contributing to its onset and progression. Identification of specific bacterial taxa associated with early stages of colorectal cancer may help develop effective microbiome-based diagnostics. For precancerous lesions, links of their characteristics to luminal and tumor-associated microbiome composition are to be elucidated. Paired stool and tumor brush biopsy samples were collected from 50 patients with precancerous lesions and early forms of colon cancer; their microbial communities were profiled using high-throughput 16S rRNA sequencing. We showed that the microbiome differences between stool and biopsy samples can be to a high extent computationally corrected. Compositionality-aware statistical analysis of microbiome composition revealed its associations with the number of lesions, lesion type, location and malignization pathway. A major determinant of precancerous lesions malignancy risk—the number of lesions—was positively associated with the abundance of H2S-producing taxa. Our results contribute to the basis for developing early non-invasive colorectal cancer diagnostics via identifying microorganisms likely participating in early stages of cancer pathogenesis.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Luminal and Tumor-Associated Gut Microbiome Features Linked to Precancerous Lesions Malignancy Risk: A Compositional Approach

Романов¹,

Karasev

Klimenko

et al. 2022

Cancers

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“…This letter is about a particular case of approximation of a compositional vector by the nearest balance—its application to principal balance analysis (PBA). It compares two methods: our NearestBalance approach ( 1 ) and the constrained method suggested previously in references 2 and 3 . We recognize that they have the same underlying idea, and we apologize for having missed this fact in our original paper.…”

Section: Lettermentioning

confidence: 99%

“…This letter was motivated by a discussion at the conference on compositional data analysis CoDaWork2022. We presented our nearest balance approach to approximation of a compositional vector ( 1 ) and mentioned its application to principal balance analysis (PBA). J.…”

Section: Lettermentioning

confidence: 99%

Note on the Difference between the Principal Balance Analysis with NearestBalance and Constrained Methods

Odintsova¹,

Klimenko

Tyakht

2023

mSystems

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Effect of Lactobacillus reuteri NCIMB 30351 drops on symptoms of infantile functional gastrointestinal disorders and gut microbiota in early infants: Results from a randomized, placebo-controlled clinical trial

Tyrsin,

Nemenov

et al. 2024

Eur J Pediatr

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Background: Infantile functional gastrointestinal disorders, such as colic, constipation, diarrhea, and gastroesophageal reflux (regurgitation), often occur in early infancy and, representing one of the causes of significant parental anxiety, lead to a significant strain on the healthcare resources.Objectives: In this study, we aimed to evaluate the effects of Lactobacillus reuteri drops (L.Reuteri NCIMB 30351) on the symptoms of infantile colic, constipation, diarrhea, and gastroesophageal reflux, as well as on the levels of intestinal microbiota in full-term newborns during the first months of life. Methods: A randomized, placebo-controlled, single-masked (blinded), post-marketing clinical study was conducted in two clinical units -Children's City Clinical Hospital of Moscow and Medical Center "St. Andrew's Hospitals -NEBOLIT" from March 2020 to May 2022 in 90 infants aged from 1 to 4 months (mean age (±SD) 12.3 ±5.09 weeks; 53.3% females, 46.7% males). Patients with colic, regurgitation (single symptom or combination of several symptoms) and constipation or diarrhea were randomly allocated in two parallel arms to receive either 5 drops (2x10^8 colony forming unit) of L. Reuteri NCIMB 30351 (n=60) or masked placebo (n=30) for 25 consecutive days. Two treatment arms had equal numbers of patients with constipation and diarrhea (n=30 each). Daily crying times and their duration, evacuations and regurgitations were recorded in a structured diary. The levels of gut microbiota were analyzed by deep sequencing of bacterial 16S rRNA gene .Results: Infants with colic receiving supplementary L. reuteri NCIMB 30351 for 25 days had significant reduction in the numbers of colic (change from baseline -6.3 (7.34) vs -3.0 (7.29) in placebo, p<0.05), numbers of crying cases and mean duration of crying (decrease from baseline -144 (70.7) minutes, lower in Diarrhea subgroup than in Constipation infants, compared with -80 (58.9) in placebo, p<0.0001), as well as regurgitations numbers (decreased by -4.8 (2.49) with L. reuteri vs -3 (7.74) with placebo). We also observed increased numbers of evacuations in infants with constipation (L. reuteri 2.2 (2.4) vs 0.9 (1.06) in placebo, p<0.05). There was a remarkable reduction of evacuations in infants with diarrhea, while not statistically significant. The analysis of bacterial 16S rRNA genes in the collected samples showed that L. reuteri positively influences the proportions of prevalent species, while negatively affects both conditionally pathogenic and commensal microbes. Additional in vitro test for formation of Clostridium colonies in the 3 presence of the probiotic demonstrated that L. reuteri effectively inhibits the growth of pathogenic Clostridium species. No adverse events were reported in this study. Conclusions:The uptake of L. Reuteri NCIMB 30351 leads to a significant reduction in the number of regurgitations, feeding-induced constipations and diarrhea as well as mean daily numbers of crying and crying duration in infants during the first months of life. Our results sugges...

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Approximation of a Microbiome Composition Shift by a Change in a Single Balance Between Two Groups of Taxa

Cited by 10 publications

References 29 publications

Luminal and Tumor-Associated Gut Microbiome Features Linked to Precancerous Lesions Malignancy Risk: A Compositional Approach

Luminal and Tumor-Associated Gut Microbiome Features Linked to Precancerous Lesions Malignancy Risk: A Compositional Approach

Note on the Difference between the Principal Balance Analysis with NearestBalance and Constrained Methods

Effect of Lactobacillus reuteri NCIMB 30351 drops on symptoms of infantile functional gastrointestinal disorders and gut microbiota in early infants: Results from a randomized, placebo-controlled clinical trial

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