# Metaphlan3 output containing a high abundance of Flavobacteriia which is not profiled by KRAKEN2 **URL:** \ **Category:** MetaPhlAn\ **Created:** [October 31, 2020, 3:50am UTC](https://forum.biobakery.org/t/metaphlan3-output-containing-a-high-abundance-of-flavobacteriia-which-is-not-profiled-by-kraken2/1217 "2020-10-31T03:50:53Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![cookiemonsterxxm](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/cookiemonsterxxm/32/454_2.png) [@cookiemonsterxxm](https://forum.biobakery.org/u/cookiemonsterxxm)\ **Post date:** [October 31, 2020, 3:50am UTC](https://forum.biobakery.org/t/metaphlan3-output-containing-a-high-abundance-of-flavobacteriia-which-is-not-profiled-by-kraken2/1217/1 "2020-10-31T03:50:53Z")
Hi, I am quite confused about the microbial profiling result given by Metaphlan3 and Kraken2. I used a mock community metagenome data(SRR8073716) to check the profiling accuracy which is deposited in: [https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8073716](https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8073716) The following result is produced from the metaphlan3, which shows the genus of Muricauda counts 73.2% while Halomonas counts3.5%: ➜ STEP3\_METAPHLAN3 grep g\_ SRR8073716.metaphlan.txt | grep -v s\_ | cut -f1,3 k\_\_Bacteria|p\_\_Bacteroidetes|c\_\_Flavobacteriia|o\_\_Flavobacteriales|f\_\_Flavobacteriaceae|g\_\_Muricauda 73.22683 k\_\_Bacteria|p\_\_Proteobacteria|c\_\_Alphaproteobacteria|o\_\_Rhizobiales|f\_\_Cohaesibacteraceae|g\_\_Cohaesibacter 19.97918 k\_\_Bacteria|p\_\_Actinobacteria|c\_\_Actinobacteria|o\_\_Micromonosporales|f\_\_Micromonosporaceae|g\_\_Micromonospora 3.88489 k\_\_Bacteria|p\_\_Proteobacteria|c\_\_Alphaproteobacteria|o\_\_Rhodobacterales|f\_\_Rhodobacteraceae|g\_\_Thioclava 2.87363 k\_\_Bacteria|p\_\_Proteobacteria|c\_\_Gammaproteobacteria|o\_\_Oceanospirillales|f\_\_Halomonadaceae|g\_\_Halomonas 0.03547 However, using kraken2, I got the genus profiling result based on a 0.0005 threshold (Halomonas counts 47%): Halomonas 0.472506522079523 Marinobacter 0.227462452145326 Psychrobacter 0.0559655089494823 Acinetobacter 0.00153809705484573 Moraxella 0.000736164818070423 Pseudomonas 0.00158863853633053 Vibrio 0.000601862188834009 Cohaesibacter 0.090182141229469 Thioclava 0.0213003156275142 Muricauda 0.067132217471038 Maribacter 0.00272361195132018 Flavobacterium 0.00219803972160995 Winogradskyella 0.0012892608573708 Cellulophaga 0.0010683676450856 Flagellimonas 0.000789178202723343 Polaribacter 0.000737527138769062 Arenibacter 0.000643674954892236 Aquimarina 0.000534621491183538 Zobellia 0.00052313114827737 Sediminicola 0.00050173469965757 Micromonospora 0.024416103338325 Streptomyces 0.000887906385118827 Compared to the [https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8073716](https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8073716), it seems like the kraken2 result may somehow be similar to the NCBI result(but I know the NCBI result is based on the NCBI [taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy) database(The database contained 48,180 taxonomy nodes in January 2017) and thus provide a more stable result. I used to use metaphlan2 a lot before in the gut microbiome research and I am currently going to update the profiling method now like trying kraken2, metaphlan2 and metaphlan3 to compare the profiling result. In the link: [MetaPhlAn 3 versus 2 -- different results](https://forum.biobakery.org/t/metaphlan-3-versus-2-different-results/680) , I thought I had a somehow similar question to this that caused a high abundance of Flavobacteriia which might be wrong. Generally speaking, I feel like metaphlan2 is stable and applicable in gut microbiome research(also many published papers proved this!) and kraken2 database contains more entries and thus caused more species in the profiling result. Any suggestion would be appreciated!! Thank you in advance!