Loading required package: phyloseq Loading required package: ggplot2 microbiome R package (microbiome.github.com) Copyright (C) 2011-2025 Leo Lahti, Sudarshan Shetty et al. Note: we recommend switching to the SummarizedExperiment framework, see microbiome.github.io/OMA and the mia package. Minimum maintenance is provided microbiome R package but the development efforts have switched to mia. Attaching package: ‘microbiome’ The following object is masked from ‘package:ggplot2’: alpha The following object is masked from ‘package:base’: transform Loading required package: permute Attaching package: ‘vegan’ The following object is masked from ‘package:microbiome’: diversity Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union [1] "ANCOMBC analysis started at 2026-05-21 16:42:14.535504" [1] "Running ANCOMBC at level Phylum" Checking the input data type ... The input data is of type: phyloseq PASS Checking the sample metadata ... The specified variables in the formula: Group009 The available variables in the sample metadata: Sample.Name, Group001, Group002, Group003, Group005, Group006, Group007, Group009, Group010, Group, Group.1 PASS Checking other arguments ... The number of groups of interest is: 2 The sample size per group is: SMT Final B PMA+ = 16, SMT Final B PMA- = 16 PASS Obtaining initial estimates ... Estimating sample-specific biases ... Loading required package: foreach Loading required package: rngtools ANCOM-BC2 primary results ... Conducting sensitivity analysis for pseudo-count addition to 0s ... For taxa that are significant but do not pass the sensitivity analysis, they are marked in the 'passed_ss' column and will be treated as non-significant in the 'diff_robust' column. For detailed instructions on performing sensitivity analysis, please refer to the package vignette. [1] "Running ANCOMBC at level Class" Checking the input data type ... The input data is of type: phyloseq PASS Checking the sample metadata ... The specified variables in the formula: Group009 The available variables in the sample metadata: Sample.Name, Group001, Group002, Group003, Group005, Group006, Group007, Group009, Group010, Group, Group.1 PASS Checking other arguments ... The number of groups of interest is: 2 The sample size per group is: SMT Final B PMA+ = 16, SMT Final B PMA- = 16 PASS Obtaining initial estimates ... Estimating sample-specific biases ... ANCOM-BC2 primary results ... Conducting sensitivity analysis for pseudo-count addition to 0s ... For taxa that are significant but do not pass the sensitivity analysis, they are marked in the 'passed_ss' column and will be treated as non-significant in the 'diff_robust' column. For detailed instructions on performing sensitivity analysis, please refer to the package vignette. [1] "Running ANCOMBC at level Order" Checking the input data type ... The input data is of type: phyloseq PASS Checking the sample metadata ... The specified variables in the formula: Group009 The available variables in the sample metadata: Sample.Name, Group001, Group002, Group003, Group005, Group006, Group007, Group009, Group010, Group, Group.1 PASS Checking other arguments ... The number of groups of interest is: 2 The sample size per group is: SMT Final B PMA+ = 16, SMT Final B PMA- = 16 PASS Obtaining initial estimates ... Estimating sample-specific biases ... ANCOM-BC2 primary results ... Conducting sensitivity analysis for pseudo-count addition to 0s ... For taxa that are significant but do not pass the sensitivity analysis, they are marked in the 'passed_ss' column and will be treated as non-significant in the 'diff_robust' column. For detailed instructions on performing sensitivity analysis, please refer to the package vignette. [1] "Running ANCOMBC at level Family" Checking the input data type ... The input data is of type: phyloseq PASS Checking the sample metadata ... The specified variables in the formula: Group009 The available variables in the sample metadata: Sample.Name, Group001, Group002, Group003, Group005, Group006, Group007, Group009, Group010, Group, Group.1 PASS Checking other arguments ... The number of groups of interest is: 2 The sample size per group is: SMT Final B PMA+ = 16, SMT Final B PMA- = 16 PASS Obtaining initial estimates ... Estimating sample-specific biases ... ANCOM-BC2 primary results ... Conducting sensitivity analysis for pseudo-count addition to 0s ... For taxa that are significant but do not pass the sensitivity analysis, they are marked in the 'passed_ss' column and will be treated as non-significant in the 'diff_robust' column. For detailed instructions on performing sensitivity analysis, please refer to the package vignette. [1] "Running ANCOMBC at level Genus" Checking the input data type ... The input data is of type: phyloseq PASS Checking the sample metadata ... The specified variables in the formula: Group009 The available variables in the sample metadata: Sample.Name, Group001, Group002, Group003, Group005, Group006, Group007, Group009, Group010, Group, Group.1 PASS Checking other arguments ... The number of groups of interest is: 2 The sample size per group is: SMT Final B PMA+ = 16, SMT Final B PMA- = 16 PASS Obtaining initial estimates ... Estimating sample-specific biases ... ANCOM-BC2 primary results ... Conducting sensitivity analysis for pseudo-count addition to 0s ... For taxa that are significant but do not pass the sensitivity analysis, they are marked in the 'passed_ss' column and will be treated as non-significant in the 'diff_robust' column. For detailed instructions on performing sensitivity analysis, please refer to the package vignette. [1] "Running ANCOMBC at level Species" Checking the input data type ... The input data is of type: phyloseq PASS Checking the sample metadata ... The specified variables in the formula: Group009 The available variables in the sample metadata: Sample.Name, Group001, Group002, Group003, Group005, Group006, Group007, Group009, Group010, Group, Group.1 PASS Checking other arguments ... The number of groups of interest is: 2 The sample size per group is: SMT Final B PMA+ = 16, SMT Final B PMA- = 16 PASS Obtaining initial estimates ... Estimating sample-specific biases ... ANCOM-BC2 primary results ... Conducting sensitivity analysis for pseudo-count addition to 0s ... For taxa that are significant but do not pass the sensitivity analysis, they are marked in the 'passed_ss' column and will be treated as non-significant in the 'diff_robust' column. For detailed instructions on performing sensitivity analysis, please refer to the package vignette. Warning messages: 1: The group variable has < 3 categories The multi-group comparisons (global/pairwise/dunnet/trend) will be deactivated 2: The group variable has < 3 categories The multi-group comparisons (global/pairwise/dunnet/trend) will be deactivated 3: The group variable has < 3 categories The multi-group comparisons (global/pairwise/dunnet/trend) will be deactivated 4: The group variable has < 3 categories The multi-group comparisons (global/pairwise/dunnet/trend) will be deactivated 5: The group variable has < 3 categories The multi-group comparisons (global/pairwise/dunnet/trend) will be deactivated 6: The group variable has < 3 categories The multi-group comparisons (global/pairwise/dunnet/trend) will be deactivated [1] TRUE [1] "ANCOMBC analysis completed at 2026-05-21 16:42:42.577792"