Thank you very much for your contributions to sequencing. I am currently engaged in metagenomic research and have recently noticed an increasing number of articles about Metaphlan4, which piqued my interest. I conducted testing with a standard sample consisting of Enterococcus faecalis (12%), Staphylococcus aureus (12%), Limosilactobacillus fermentum (12%), Listeria monocytogenes (12%), Salmonella enterica (12%), Escherichia coli (12%), Pseudomonas aeruginosa (12%), Bacillus subtilis (12%), Saccharomyces cerevisiae (2%), and Cryptococcus neoformans (2%). However, the annotation results from Metaphlan show discrepancies in the relative abundances compared to the Zymo standard sample manual (with screenshots comparing the manual’s proportions and the annotation results). Additionally, Bacillus subtilis (12%) is not annotated (marked in red), which is quite confusing. Attached are the standard sample information (manual), the reference genome of Bacillus subtilis (provided by Zymo), and the raw data from the standard sample test. Please help explain: 1) The reasons for the deviation in species relative abundance. 2) The reason Metaphlan4’s database does not annotate Bacillus subtilis.
Here is the translated text:
We are using software version 4.0.6. humann3 script is:
humann3 --minpath off --gap-fill on --threads 5 --protein-database HUMAnN3/uniref90_v201901b -i metatest.6.fq.gz -o metacyc --output-basename metatest.6 --metaphlan-options “-t rel_ab_w_read_stats”
metaphlan log ：/miniconda3/envs/humann3/bin/metaphlan humann_temp/tmp_tgskhry/tmp3zzzvzlz -t rel_ab_w_read_stats -o metatest.6_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out metatest.6_metaphlan_bowtie2.txt --nproc 5
I can provide the specific sequencing sequence files and send them via email. What email address should I send them to? My email is 529461767@qq.com.