overview

phyloseq object

OTU table should be prepared, metadata and taxonomic table details

Example: phyloseq

The diet swap data set represents a study with African and African American groups undergoing a two-week diet swap. For details, see https://www.nature.com/articles/ncomms7342.

phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 130 taxa and 222 samples ]
sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 130 taxa by 3 taxonomic ranks ]

Looking into the data

• Number of taxonomic groups: 130

• Number of samples: 222

• Number of metadata fields: 8:

• Metadata variables are: subject, sex, nationality, group, sample, timepoint, timepoint.within.group, bmi_group

Unique taxa at Phylum:

phyloseq::get_taxa_unique(phy, “Phylum”)
Actinobacteria
Firmicutes
Proteobacteria
Verrucomicrobia
Bacteroidetes
Spirochaetes
Fusobacteria
Cyanobacteria

Unique taxa at Genus:

phyloseq::get_taxa_unique(phy, “Genus”)
Actinomycetaceae
Aerococcus
Aeromonas
Akkermansia
Alcaligenes faecalis et rel.
Allistipes et rel.
Anaerobiospirillum
Anaerofustis
Anaerostipes caccae et rel.
Anaerotruncus colihominis et rel.
Anaerovorax odorimutans et rel.
Aneurinibacillus
Aquabacterium
Asteroleplasma et rel.
Atopobium
Bacillus
Bacteroides fragilis et rel.
Bacteroides intestinalis et rel.
Bacteroides ovatus et rel.
Bacteroides plebeius et rel.
Bacteroides splachnicus et rel.
Bacteroides stercoris et rel.
Bacteroides uniformis et rel.
Bacteroides vulgatus et rel.
Bifidobacterium
Bilophila et rel.
Brachyspira
Bryantella formatexigens et rel.
Bulleidia moorei et rel.
Burkholderia
Butyrivibrio crossotus et rel.
Campylobacter
Catenibacterium mitsuokai et rel.
Clostridium (sensu stricto)
Clostridium cellulosi et rel.
Clostridium colinum et rel.
Clostridium difficile et rel.
Clostridium felsineum et rel.
Clostridium leptum et rel.
Clostridium nexile et rel.
Clostridium orbiscindens et rel.
Clostridium ramosum et rel.
Clostridium sphenoides et rel.
Clostridium stercorarium et rel.
Clostridium symbiosum et rel.
Clostridium thermocellum et rel.
Collinsella
Coprobacillus catenaformis et rel.
Coprococcus eutactus et rel.
Corynebacterium
Desulfovibrio et rel.
Dialister
Dorea formicigenerans et rel.
Eggerthella lenta et rel.
Enterobacter aerogenes et rel.
Enterococcus
Escherichia coli et rel.
Eubacterium biforme et rel.
Eubacterium cylindroides et rel.
Eubacterium hallii et rel.
Eubacterium limosum et rel.
Eubacterium rectale et rel.
Eubacterium siraeum et rel.
Eubacterium ventriosum et rel.
Faecalibacterium prausnitzii et rel.
Fusobacteria
Gemella
Granulicatella
Haemophilus
Helicobacter
Klebisiella pneumoniae et rel.
Lachnobacillus bovis et rel.
Lachnospira pectinoschiza et rel.
Lactobacillus catenaformis et rel.
Lactobacillus gasseri et rel.
Lactobacillus plantarum et rel.
Lactobacillus salivarius et rel.
Lactococcus
Leminorella
Megamonas hypermegale et rel.
Megasphaera elsdenii et rel.
Methylobacterium
Micrococcaceae
Mitsuokella multiacida et rel.
Moraxellaceae
Novosphingobium
Oceanospirillum
Oscillospira guillermondii et rel.
Outgrouping clostridium cluster XIVa
Oxalobacter formigenes et rel.
Papillibacter cinnamivorans et rel.
Parabacteroides distasonis et rel.
Peptococcus niger et rel.
Peptostreptococcus anaerobius et rel.
Peptostreptococcus micros et rel.
Phascolarctobacterium faecium et rel.
Prevotella melaninogenica et rel.
Prevotella oralis et rel.
Prevotella ruminicola et rel.
Prevotella tannerae et rel.
Propionibacterium
Proteus et rel.
Pseudomonas
Roseburia intestinalis et rel.
Ruminococcus bromii et rel.
Ruminococcus callidus et rel.
Ruminococcus gnavus et rel.
Ruminococcus lactaris et rel.
Ruminococcus obeum et rel.
Serratia
Sporobacter termitidis et rel.
Staphylococcus
Streptococcus bovis et rel.
Streptococcus intermedius et rel.
Streptococcus mitis et rel.
Subdoligranulum variable at rel.
Sutterella wadsworthia et rel.
Tannerella et rel.
Uncultured Bacteroidetes
Uncultured Chroococcales
Uncultured Clostridiales I
Uncultured Clostridiales II
Uncultured Mollicutes
Uncultured Selenomonadaceae
Veillonella
Vibrio
Weissella et rel.
Wissella et rel.
Xanthomonadaceae
Yersinia et rel.

Useful plots

The taxa ranks in the previous phyloseq dataset are: Phylum, Family, Genus

Important to remember taxa abundances are compositional that are need appropriate transform to be informative, here I will use the relative abundances via compositional transform.

Abundance at Phylum level

Abundance at Family level

Abundance at Genus level

Heatmaps for the core taxa with certain prevalences & detections

Core heatmaps

Acknowledgement to "Leo Lahti, Sudarshan Shetty et al. (2017). Tools for microbiome analysis in R. Version . URL: http://microbiome.github.com/microbiome