Microbial Composition for Gut Microbiome Recovery
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Solution Overview
Problem
The recovery of the gut microbiome after antibiotic usage is slow and variable, and the specific microbial species and functions that facilitate or impede this process are not well understood, with existing probiotics showing unclear utility and potential to delay recovery.
Innovation Solution
A metagenome-wide association approach identifies microbial species such as Bacteroides thetaiotaomicron and Bifidobacterium adolescentis that facilitate carbohydrate degradation and cross-feeding, providing a synergistic boost to microbial abundance and diversity through a composition comprising these species, which can be administered to treat or decrease gut microbiome dysbiosis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If commonly used probiotics are administered after antibiotic treatment, then host health may be generally beneficial, but microbiome recovery may be delayed
Solution Approach 1:
The patent extracts and identifies specific microbial species and functions from the complex probiotic mixture that are真正 responsible for facilitating microbiome recovery. By isolating these key players (such as carbohydrate-degrading species), the invention removes the harmful delay effect while preserving the beneficial health effects, resolving the contradiction between probiotic administration and recovery speed.
Solution Approach 2:
The patent introduces carbohydrate-degrading microbial species as intermediaries that break down complex carbohydrates into simpler compounds, which then serve as substrates for other microbiome members. This intermediary action facilitates the reconstruction of microbial food webs and accelerates recovery, allowing probiotic administration to benefit health without delaying recovery.
2Reliability
If high initial diversity in the gut microbiome is present, then better recovery from antibiotic-induced perturbations occurs, but the specific species and functions facilitating recovery are not well understood
Solution Approach 1:
The patent segments the complex microbiome recovery process into specific functional categories, particularly carbohydrate degradation capabilities. By dividing the diverse microbial community into functional groups based on their metabolic roles, the invention identifies which specific species and functions (carbohydrate-degrading enzymes, cross-feeding interactions) are critical for recovery, thereby recovering the lost information about mechanisms while maintaining the benefit of high diversity.
Solution Approach 2:
The patent changes the analytical parameter from simply measuring microbial diversity to measuring specific functional capabilities, particularly carbohydrate degradation activity. This parameter shift reveals that it is not just the presence of diverse species but their specific metabolic functions (carbohydrate breakdown, cross-feeding) that drive recovery, thus recovering the mechanistic information needed to understand and enhance recovery outcomes.
3Reliability
If antibiotic treatment is administered, then infections are treated, but profound and long-term alterations to the gut microbiome occur
Solution Approach 1:
The patent applies preliminary action by administering specific carbohydrate-degrading microbial species immediately after antibiotic treatment to preemptively kickstart the recovery process. These pre-administered species begin degrading carbohydrates and rebuilding food webs before the microbiome can fully collapse, thereby counteracting the destabilizing effect of antibiotics and facilitating faster restoration of microbiome composition stability.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The identified microbial species significantly enhance microbial abundance and diversity, promoting robust recovery of the gut microbiome by degrading host- and diet-derived carbohydrates, rebuilding the food web and accelerating the return to healthy microbial community structure.
Implementation Method 1
These selected microorganisms have been shown to possess specific functions that facilitate recovery, including carbohydrate degradation
Implementation Method 2
Alistipes shahii, Bacteroides caccae, Bacteroides coprocola, Bacteroides eggerthii, Bacteroides intestinalis, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium longum, Coprococcus catus, Desulfovibrio piger, Faecalibacterium prausnitzii, Parabacteroides distasonis, Parabacteroides johnsonii, Roseburia inulinivorans, Ruminococcus bromii, Ruminococcus torques, and Subdoligranulum variabile. These selected microorganisms have been shown to possess specific functions that facilitate recovery, including carbohydrate degradation and cross-feeding
Data Source
AI summary
The invention relates to using a class of microbial species that can contribute to robust recovery of the microbiome after antibiotic usage. In particular, the inventors of this invention have identified 21 bacterial species exhibiting robust association with ecological recovery post antibiotic therapy. As such, in an aspect of the invention, there is provided a use of composition comprising at least one of or any combination of microorganisms selected from the group consisting of: Bacteroides thetaiotaomicron, Bifidobacterium adolescentis, Alistipes putredinis, Alistipes shahii, Bacteroides caccae, Bacteroides coprocola, Bacteroides eggerthii, Bacteroides intestinalis, Bacteroides stercoris, Bacteroides uniformis, Bifidobacterium bifidum, Bifidobacterium longum, Coprococcus catus, Desulfovibrio piger, Faecalibacterium prausnitzii, Parabacteroides distasonis, Parabacteroides johnsonii, Roseburia inulinivorans, Ruminococcus bromii, Ruminococcus torques, and Subdoligranulum variabile for treating or decreasing gut microbiome dysbiosis induced by a prior antibiotic treatment.