Sometimes we do RNA-seq of biopsy from the inflammation tissue and there sometimes are bacterias in it. Would it influence the results of tissues or not? If so, how to distinguish between bacteria and inflammation tissues by RNA-seq?
I will assume a lot, because you didn't provide much information. If you provide more information, we could potentially come up with more appropriate answers.
If you are doing Illumina library prep with a polyA tail capture kit - which is the more common option, so a reasonable assumption - and your RNA is of good quality, contamination should be minimal. If the RNA is degraded, I've seen polyA capture protocol not working properly and being non-specific, that is, picking non-polyA stuff, like ribosomal RNA or bacterial RNA.
If you are mapping to the human genome - another reasonable assumption - most bacterial reads wouldn't map, and would most likely have a negligible effect on your downstream analyses. Check the mapping quality for issues, but the mapping rate alone should be good indication if the sample is good or bad - for RNAseq, I would expect at least 80% reads mapping to the human genome.
However, even contamination being unlikely or negligible, you should keep track of which samples have only inflammation, and which have inflammation + infection, as this could have a huge impact on differential gene expression analyses.
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You can use contaminant checks/metagenomic tools (kraken with transcriptome-database, centrifuge, k-Slam, ...) to resolve or at least quantify this.