Cell | over 100 strains! Design and construction of ultra-complex synthetic intestinal microbial communities

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As the field of microbiome continues to evolve, current research has gradually shifted from correlation studies to causal studies

Although the microbiota samples used in the fecal bacteria transplantation method reflect the true situation of the human gut microbiota to the greatest extent, their composition is unknown, and it is difficult to dissect the specific microorganisms

These limitations have hindered the development of microbiome research to some extent, so there is an urgent need to develop synthetic microbial communities with clear composition and higher complexity to better promote the development

On September 6, 2022, a team of Michael A.

First, the authors screened microbes (both high and low abundance)

All 104 strains mentioned above can be grown

To accurately detect the relative abundance of different strains in this community, the authors used metagenomic sequencing for sequencing

Based on metagenomic sequencing and the NinjaMap method, the authors first assessed the stability
of this synthetic community, hCom1.

The authors incubated this community in SAAC medium for 48 h and examined microbial composition at 0, 12, 24, and 48 h
, respectively.

The results show that after 12h of incubation, hCom1 has tended to stabilize, and multiple biological replicates and technical replicates have shown similar composition, indicating that hCom1 has high stability
.

The authors then used this system to explore the strain-nutrient map
.

There have been many studies exploring the use of polysaccharides by the gut microbiota, but the use of amino acids by the gut microbiome is still poorly
understood.

The authors explored this problem
using 20 specific growth media (lacking one amino acid).

The results showed that the deficiency of most amino acids had less
effect on the constituent strains of hCom1.

At the same time, the study validated some of the previous findings that methionine promotes the growth
of Anaerostipes caccae.

This result shows that although there will be nutritional competition between different microorganisms in a community, the effect
of limiting an amino acid on different strains in the community can still be observed.

The study also found that deficiencies in certain amino acids can have a significant effect on the growth of microorganisms, such as more than half of the strains respond
to cysteine deficiencies.

Subsequently, the authors transplanted hCom1 into germ-free mice and collected feces from mice for 8 weeks
.

Analysis of the fecal flora of mice showed that: (1) most of the strains were able to colonize successfully, and only 3 strains were undetected; (2) hCom1 can quickly reach a stable state in vivo, and the composition of the microflora at 2 weeks is highly similar
to the test results at 8 weeks.

To better simulate the real gut flora, the authors added strains to hCom1 to fill the niche gap
.

Based on the principle of colonization resistance, the authors first transplanted hCom1 to germ-free mice, and after 4 weeks, they gave mice a human fecal challenge test, that is, a human fecal sample (Hum1-3)
was given to mice.

After another 4 weeks, metagenomic sequencing was used to analyze fecal composition
.

The results showed that 89% of the strains were derived from hCom1 and 11% were new members
.

The authors screened 24 candidate bacterial strains from new members as a supplement, 22 of which could be successfully cultured
.

Since there were 7 hCom1-derived strains that were replaced during the experiment, based on this, the authors selected the remaining 97 strains of hCom1 and 22 new members for a total of 119 strains to form hCom2
.

To assess the integrity of hCom2, the authors conducted a challenge trial
using the same samples of human fecal bacteria.

The results show that compared with hCom1, the colonization resistance of hCom2 is significantly enhanced, and the changes before and after the challenge are small, indicating that the integrity and stability of hCom2 are better
.

Further evaluations showed that different mice of the same strain colonized hCom2 and mice of different strains had similar fecal compositions, indicating better biogibility
.

And compared with mice colonized with human fecal bacteria, not only are the microbial cells of the two microbial cells similar, but also have a similar phenotype, that is, the colonic immune profile and the microbiota metabolism profile of the two mice are similar
.

Finally, the authors assessed the availability of hCom2 as a model, testing hCom2 resistance to pathogens and pathogenic commensal bacteria
.

The authors used intestinal hemorrhagic E.
coli ATCC 43894 (EHEC) to measure colonization resistance to hCom2
.

The results showed that the colonization resistance of mice colonizing hCom2 and HCOM2 was similar to that of HCOM2, and both were able to effectively resist the colonization
of EHEC.

In addition, by rejecting certain phylums in hCom2, the authors also found that microbes from the Phylum Pachyderma play an important role
in the process of resisting EEC.

In summary, the study successfully established an artificial synthetic community with clear composition, high complexity and good reflection of the real human intestinal flora, providing a new means
for microbiome research.

However, the system can be further improved in the future, including the inclusion of more bacterial strains to fill the remaining ecological niches, as well as the addition of intestinal flora members
such as fungi, archaea and viruses.

Model Maker: Eleven

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