Case 1 Integration study of human intestinal microbial macrogenome and macrotranscriptome
Research background:
In this study, the first human microbiome study was carried out using the human multi-site samples collected by the subjects themselves, combined with phenotypic taxonomy, macrogenomics and metatranscriptional spectrum. Results The relationship between the genomic potential and gene expression of intestinal flora was described in detail, and the feasibility of conducting macro transcriptome research in the samples collected and transported by the subjects was demonstrated.
Research results:
The method of self-collection has little impact on the study of genomics, and can provide representative macrogenome and macrotranscriptome data.
Taking KO database as a reference, 3292 relative abundances of DNA and RNA were finally obtained, and the level of DNA and RNA was correlated. The results showed that the abundance of genes and transcripts had a good correlation.
Although the composition of macrogenomes among different individuals is relatively conservative, they differ at the macro transcriptome level, indicating that there is a specific regulation mode of macrogenomes.

Figure 1. Different sample processing methods get the same species composition and gene function classification
Research conclusion:
This study developed a new method to collect saliva and feces for genome and transcriptome analysis. This method does not require professional personnel and facilities, but also can maintain the integrity of samples, which will enable us to carry out longitudinal research and large-scale collection research without geographical restrictions. This method also provides important insights into the genetic composition of digestive tract microbiome and bacteria related to celiac disease, oral cancer, periodontitis and obesity.
Case 2 Macrotranscriptome sequencing technology reveals that grass carp intestinal microorganisms have the ability to decompose biomass
Research background:
Most animals can decompose some specific plant polysaccharides only with the help of symbiotic bacteria in the gastrointestinal tract. Macrogenomics research has found that there are a large number of cellulolytic bacteria in the gastrointestinal tract of animals, as well as many glycoside hydrolase genes and carbohydrate binding genes. These results indicate that gastrointestinal symbiotic bacteria may participate in the decomposition process of plant polysaccharides. However, the bacteria that can decompose cellulose found in macrogenomics research are also abundant in the environment, and the glycoside hydrolase gene and carbohydrate binding gene found may not be expressed in the gastrointestinal tract. RNA-seq can be used to determine whether these genes are expressed in the gastrointestinal tract.
Research methods:
The RNA-seq technique was used to sequence 11 grass carp hindgut samples, including 3 grass carp hindgut samples fed with fish food (FM), 3 grass carp hindgut samples fed with crude fiber (CF), 3 grass carp hindgut samples fed with Sudan grass (SG), and 2 wild grass carp hindgut samples (DR, LL). By comparing the macrotranscriptome of different samples, the species composition and functional activity of microorganisms in grass carp hindgut were revealed, and the similarities and differences of grass carp hindgut macrotranscriptome under different feeding modes were further compared.
Research results:
1. Through the macro transcriptome sequencing of 11 samples, a total of 676M reads (average read length 77-98 bp) and 62 Gb optimized data were obtained.
2. The results of macrotranscriptome showed that the most important microbial populations in the hindgut of grass carp belonged to the phylum Chlamydomonas, Clostridium, Proteobacteria and Bacteroides. Archaea is rare in the hindgut of grass carp, and the most important archaea is methanogen. There were significant differences in transcripts of grass carp hindgut between Clostridium and Proteus in different feeding modes.
3. Through the analysis of all transcripts of orthologous protein clusters, it was found that there were significant differences in carbohydrate transfer and metabolism of grass carp hindgut transcripts with different feeding methods.
4. Through the annotation analysis of carbohydrate active enzyme family, it is found that the glycoside hydrolase that decomposes extracellular polysaccharides accounts for a high proportion in the transcript, indicating that grass carp hindgut microorganisms participate in the decomposition and metabolism of carbohydrates, thus providing energy for grass carp and microorganisms.


Legend interpretation: The above figure shows the annotation results of species composition of 11 sample macrotranscriptome; In the left figure, the annotation results of orthologous protein clusters (COGs) of 11 samples' macro transcriptome; The following figure on the right shows the abundance of the most important COGs in the intestines of grass carp fed with different ways.
reference:
1. Franzosa E A, Morgan X C, Segata N, et al. Relating the metatranscriptome and metagenome of the human gut[J]. Proc Natl Acad Sci U S A, 2014, 111(22): E2329.
2.Shangong Wu,Yi Ren,et al.Metatranscriptomic discovery of plant biomass-degrading capacity from grasscarp intestinal microbiomes[J]. FEMS Microbiology Ecology.