Strange issue when importing data

[msuokas-bco]

I accidentally run into this when importing same set of data to both phyloseq and TreeSummarizedExperiment

For both, same count and taxonomy dataframes were used. Rows 13 & 14 are without obvious reason inverted when I create phyloseq object. If there are any other differences, they might not be visible in later analysis. Shifting of rows doesn't explain difference, as other surrounding taxa are in perfect order.

Here is snippet from original taxonomy df

13	Bacteria	Bacteroidota	Bacteroidia	Bacteroidales	Paludibacteraceae	Microbacter	NA
14	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	Aeromonas	NA

After

pseq_vsearch99 <- phyloseq(otu_table(vs99, taxa_are_rows = TRUE),
tax_table(otu_taxonomy))

Here is result from my phyloseq tax_table on rows 12 and 15
domain phylum class order
2d04fc8ffd795de26302731f97932768b6a31d7e "Bacteria" "Firmicutes" "Clostridia" "Lachnospirales"
348ce5376df891470a91f589a67d3d617aafd2d6 "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Aeromonadales"
2f2bd0fd6ef68543a7a28d9802aaf42b5a8970f6 "Bacteria" "Bacteroidota" "Bacteroidia" "Bacteroidales"
0ec7e69cf4de920d84fe68fef17f9af4420d5a80 "Bacteria" "Firmicutes" "Clostridia" "Clostridiales"
family genus species
2d04fc8ffd795de26302731f97932768b6a31d7e "Lachnospiraceae" NA NA
348ce5376df891470a91f589a67d3d617aafd2d6 "Aeromonadaceae" "Aeromonas" NA
2f2bd0fd6ef68543a7a28d9802aaf42b5a8970f6 "Paludibacteraceae" "Microbacter" NA
0ec7e69cf4de920d84fe68fef17f9af4420d5a80 "Clostridiaceae" "Clostridium sensu stricto 13" NA

And this is what I get from tse rowData

                                          domain         phylum               class          order            family
                                     <character>    <character>         <character>    <character>       <character>

2d04fc8ffd795de26302731f97932768b6a31d7e Bacteria Firmicutes Clostridia Lachnospirales Lachnospiraceae
348ce5376df891470a91f589a67d3d617aafd2d6 Bacteria Bacteroidota Bacteroidia Bacteroidales Paludibacteraceae
2f2bd0fd6ef68543a7a28d9802aaf42b5a8970f6 Bacteria Proteobacteria Gammaproteobacteria Aeromonadales Aeromonadaceae
0ec7e69cf4de920d84fe68fef17f9af4420d5a80 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae
genus species

2d04fc8ffd795de26302731f97932768b6a31d7e NA NA
348ce5376df891470a91f589a67d3d617aafd2d6 Microbacter NA
2f2bd0fd6ef68543a7a28d9802aaf42b5a8970f6 Aeromonas NA
0ec7e69cf4de920d84fe68fef17f9af4420d5a80 Clostridium sensu st.. NA