Chapter 7 Functional differences
# Aggregate bundle-level GIFTs into the compound level
GIFTs_elements <- to.elements(genome_gifts, GIFT_db)
GIFTs_elements_filtered <- GIFTs_elements[rownames(GIFTs_elements) %in% genome_counts$genome, ]
GIFTs_elements_filtered <- as.data.frame(GIFTs_elements_filtered) %>%
select_if(~ !is.numeric(.) || sum(.) != 0)
elements <- GIFTs_elements_filtered %>%
as.data.frame()
# Aggregate element-level GIFTs into the function level
GIFTs_functions <- to.functions(GIFTs_elements_filtered, GIFT_db)
functions <- GIFTs_functions %>%
as.data.frame()
# Aggregate function-level GIFTs into overall Biosynthesis, Degradation and Structural GIFTs
GIFTs_domains <- to.domains(GIFTs_functions, GIFT_db)
domains <- GIFTs_domains %>%
as.data.frame()
# Get community-weighed average GIFTs per sample
GIFTs_elements_community <- to.community(GIFTs_elements_filtered, genome_counts_filt %>% column_to_rownames(., "genome") %>% tss(), GIFT_db)
GIFTs_functions_community <- to.community(GIFTs_functions, genome_counts_filt %>% column_to_rownames(., "genome") %>% tss(), GIFT_db)
GIFTs_domains_community <- to.community(GIFTs_domains, genome_counts_filt %>% column_to_rownames(., "genome") %>% tss(), GIFT_db)7.1 Function level
GIFTs_functions_community %>%
as.data.frame() %>%
rownames_to_column(var="sample") %>%
pivot_longer(!sample,names_to="trait",values_to="gift") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
ggplot(aes(x=trait,y=sample,fill=gift)) +
geom_tile(colour="white", size=0.2)+
scale_fill_gradientn(colours=rev(c("#d53e4f", "#f46d43", "#fdae61", "#fee08b", "#e6f598", "#abdda4", "#ddf1da")))+
facet_grid(type ~ ., scales="free",space="free")
7.1.1 GIFT test
GIFTs_functions_community_tt <- GIFTs_functions_community %>%
as.data.frame() %>%
rownames_to_column("sample") %>%
separate(sample, into = c("individual", "type"), sep = "\\.") %>%
pivot_longer(-c(individual, type), names_to = "trait", values_to = "value") %>%
group_by(trait) %>%
mutate(model_result = list(lmerTest::lmer(value ~ type + (1 | individual)))) %>%
ungroup() %>%
select(trait,model_result) %>%
unique() %>%
mutate(estimate = map_dbl(model_result, ~broom.mixed::tidy(.) %>% filter(term == "typefeces") %>% pull(estimate))) %>%
mutate(p_value = map_dbl(model_result, ~broom.mixed::tidy(.) %>% filter(term == "typefeces") %>% pull(p.value))) %>%
mutate(p_value_adj = p.adjust(p_value, method = "bonferroni")) %>%
left_join(GIFT_db %>% select(Code_function,Function) %>% unique(),by=join_by(trait==Code_function)) %>%
rename(id=trait,trait=Function) %>%
select(id,trait, estimate, p_value_adj)
GIFTs_functions_community_tt %>% tt() |>
style_tt(
i = which(GIFTs_functions_community_tt$estimate < 0 & GIFTs_functions_community_tt$p_value_adj < 0.05),
background = "#E5D5B1") |>
style_tt(
i = which(GIFTs_functions_community_tt$estimate > 0 & GIFTs_functions_community_tt$p_value_adj < 0.05),
background = "#B7BCCE")| id | trait | estimate | p_value_adj |
|---|---|---|---|
| B01 | Nucleic acid biosynthesis | -0.159859172 | 3.056969e-02 |
| B02 | Amino acid biosynthesis | -0.110393771 | 7.176260e-01 |
| B03 | Amino acid derivative biosynthesis | -0.005675742 | 1.000000e+00 |
| B04 | SCFA biosynthesis | -0.101802836 | 9.451665e-02 |
| B06 | Organic anion biosynthesis | -0.142419002 | 8.690010e-07 |
| B07 | Vitamin biosynthesis | -0.245911630 | 1.417697e-03 |
| B08 | Aromatic compound biosynthesis | -0.075353117 | 1.000000e+00 |
| B09 | Metallophore biosynthesis | 0.024252618 | 9.856097e-04 |
| B10 | Antibiotic biosynthesis | 0.016871838 | 9.042655e-04 |
| D01 | Lipid degradation | 0.024068845 | 1.000000e+00 |
| D02 | Polysaccharide degradation | 0.225103688 | 8.086379e-03 |
| D03 | Sugar degradation | 0.160719202 | 1.837959e-02 |
| D05 | Amino acid degradation | -0.061015780 | 9.915551e-02 |
| D06 | Nitrogen compound degradation | 0.069239014 | 6.663246e-04 |
| D07 | Alcohol degradation | -0.054220812 | 1.000000e+00 |
| D08 | Xenobiotic degradation | 0.014284632 | 3.645558e-02 |
| D09 | Antibiotic degradation | -0.051783327 | 1.000000e+00 |
| S01 | Cellular structure | -0.059312854 | 1.000000e+00 |
| S02 | Appendages | -0.047454351 | 1.000000e+00 |
| S03 | Spore | -0.041956134 | 1.000000e+00 |
7.1.2 GIFT test visualisation
GIFTs_functions_community %>%
as.data.frame() %>%
rownames_to_column("sample") %>%
separate(sample, into = c("individual", "type"), sep = "\\.") %>%
pivot_longer(-c(individual, type), names_to = "trait", values_to = "value") %>%
mutate(trait = case_when(
trait %in% GIFT_db$Code_function ~ GIFT_db$Function[match(trait, GIFT_db$Code_function)],
TRUE ~ trait
)) %>%
mutate(trait=factor(trait,levels=unique(GIFT_db$Function))) %>%
ggplot(aes(x=value, y=type, group=type, fill=type, color=type)) +
geom_boxplot() +
scale_color_manual(name="Sample type",
breaks=c("cloaca","feces"),
labels=c("Cloaca","Faeces"),
values=c("#e5bd5b", "#6b7398")) +
scale_fill_manual(name="Sample type",
breaks=c("cloaca","feces"),
labels=c("Cloaca","Faeces"),
values=c("#e5bd5b50", "#6b739850")) +
facet_grid(trait ~ ., space="free", scales="free") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
strip.text.y = element_text(angle = 0)) +
labs(y="Traits",x="Metabolic capacity index")
7.2 Element level
GIFTs_elements_community %>%
as.data.frame() %>%
rownames_to_column(var="sample") %>%
pivot_longer(!sample,names_to="trait",values_to="gift") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
mutate(functionid = substr(trait, 1, 3)) %>%
mutate(trait = case_when(
trait %in% GIFT_db$Code_element ~ GIFT_db$Element[match(trait, GIFT_db$Code_element)],
TRUE ~ trait
)) %>%
mutate(functionid = case_when(
functionid %in% GIFT_db$Code_function ~ GIFT_db$Function[match(functionid, GIFT_db$Code_function)],
TRUE ~ functionid
)) %>%
mutate(trait=factor(trait,levels=unique(GIFT_db$Element))) %>%
mutate(functionid=factor(functionid,levels=unique(GIFT_db$Function))) %>%
ggplot(aes(x=sample,y=trait,fill=gift)) +
geom_tile(colour="white", linewidth=0.2)+
scale_fill_gradientn(colours=rev(c("#d53e4f", "#f46d43", "#fdae61", "#fee08b", "#e6f598", "#abdda4", "#ddf1da")))+
facet_grid(functionid ~ type, scales="free",space="free") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
strip.text.y = element_text(angle = 0)) +
labs(y="Traits",x="Samples",fill="GIFT")
7.2.1 GIFT test
GIFTs_elements_community_tt <- GIFTs_elements_community %>%
as.data.frame() %>%
rownames_to_column("sample") %>%
separate(sample, into = c("individual", "type"), sep = "\\.") %>%
pivot_longer(-c(individual, type), names_to = "trait", values_to = "value") %>%
group_by(trait) %>%
mutate(model_result = list(lmerTest::lmer(value ~ type + (1 | individual)))) %>%
ungroup() %>%
select(trait,model_result) %>%
unique() %>%
mutate(estimate = map_dbl(model_result, ~broom.mixed::tidy(.) %>% filter(term == "typefeces") %>% pull(estimate))) %>%
mutate(p_value = map_dbl(model_result, ~broom.mixed::tidy(.) %>% filter(term == "typefeces") %>% pull(p.value))) %>%
mutate(p_value_adj = p.adjust(p_value, method = "bonferroni")) %>%
left_join(GIFT_db %>% select(Code_element,Element) %>% unique(),by=join_by(trait==Code_element)) %>%
rename(id=trait,trait=Element) %>%
select(id,trait, estimate, p_value_adj)
GIFTs_elements_community_tt %>% tt() |>
style_tt(
i = which(GIFTs_elements_community_tt$estimate < 0 & GIFTs_elements_community_tt$p_value_adj < 0.05),
background = "#E5D5B1") |>
style_tt(
i = which(GIFTs_elements_community_tt$estimate > 0 & GIFTs_elements_community_tt$p_value_adj < 0.05),
background = "#B7BCCE")| id | trait | estimate | p_value_adj |
|---|---|---|---|
| B0101 | Inosinic acid (IMP) | -0.151236188 | 9.039137e-04 |
| B0102 | Uridylic acid (UMP) | -0.094812312 | 1.000000e+00 |
| B0103 | UDP/UTP | -0.078774552 | 1.273680e-04 |
| B0104 | CDP/CTP | -0.291124228 | 1.894078e-01 |
| B0105 | ADP/ATP | -0.217775882 | 3.148082e-02 |
| B0106 | GDP/GTP | -0.125431870 | 1.000000e+00 |
| B0204 | Serine | -0.407615768 | 7.121696e-04 |
| B0205 | Threonine | -0.104078962 | 1.000000e+00 |
| B0206 | Cysteine | -0.057144737 | 1.000000e+00 |
| B0207 | Methionine | -0.080974853 | 1.000000e+00 |
| B0208 | Valine | -0.104574494 | 1.000000e+00 |
| B0209 | Isoleucine | -0.132603069 | 1.000000e+00 |
| B0210 | Leucine | -0.300307892 | 7.159663e-03 |
| B0211 | Lysine | -0.188989369 | 7.751700e-04 |
| B0212 | Arginine | -0.120559972 | 1.000000e+00 |
| B0213 | Proline | 0.030641621 | 1.000000e+00 |
| B0214 | Glutamate | -0.121294193 | 1.000000e+00 |
| B0215 | Histidine | -0.158359034 | 1.000000e+00 |
| B0216 | Tryptophan | -0.222953618 | 1.000000e+00 |
| B0217 | Phenylalanine | 0.104654741 | 5.429839e-03 |
| B0218 | Tyrosine | -0.070415175 | 1.000000e+00 |
| B0219 | GABA | 0.010264623 | 2.957984e-04 |
| B0220 | Beta-alanine | 0.061908085 | 1.000000e+00 |
| B0221 | Ornithine | -0.075999324 | 1.000000e+00 |
| B0302 | Betaine | 0.007429289 | 6.107924e-02 |
| B0303 | Ectoine | -0.084897201 | 1.000000e+00 |
| B0307 | Spermidine | 0.001525887 | 1.000000e+00 |
| B0309 | Putrescine | 0.026195706 | 4.093011e-04 |
| B0310 | Tryptamine | 0.008262580 | 7.302535e-01 |
| B0401 | Acetate | -0.105801039 | 1.000000e+00 |
| B0402 | Butyrate | -0.106374700 | 1.000000e+00 |
| B0403 | Propionate | -0.090489652 | 5.228183e-02 |
| B0601 | Succinate | -0.236011819 | 1.219833e-02 |
| B0602 | Fumarate | -0.185345084 | 1.412915e-03 |
| B0603 | Citrate | -0.144668012 | 4.297163e-02 |
| B0604 | L-lactate | 0.269612255 | 1.000000e+00 |
| B0605 | D-lactate | 0.162110506 | 1.000000e+00 |
| B0701 | Thiamine (B1) | -0.467508286 | 2.093102e-05 |
| B0702 | Riboflavin (B2) | -0.094914710 | 1.000000e+00 |
| B0703 | Niacin (B3) | -0.144515836 | 1.442833e-05 |
| B0704 | Pantothenate (B5) | -0.132006523 | 1.000000e+00 |
| B0705 | Pyridoxal-P (B6) | -0.136554096 | 1.000000e+00 |
| B0706 | Biotin (B7) | -0.505291636 | 6.783663e-05 |
| B0707 | Tetrahydrofolate (B9) | -0.183686244 | 5.399698e-02 |
| B0708 | Cobalamin (B12) | -0.351214616 | 5.121565e-09 |
| B0709 | Tocopherol/tocotorienol (E) | 0.051315283 | 1.768034e-03 |
| B0710 | Phylloquinone (K1) | 0.009625337 | 1.000000e+00 |
| B0711 | Menaquinone (K2) | -0.094429175 | 3.872932e-02 |
| B0712 | Ubiquinone (Q10) | -0.041293838 | 3.152997e-07 |
| B0801 | Salicylate | 0.004992759 | 1.000000e+00 |
| B0802 | Gallate | -0.056848209 | 1.000000e+00 |
| B0803 | Chorismate | -0.204713195 | 5.034798e-01 |
| B0804 | Dipicolinate | -0.179083253 | 6.017894e-01 |
| B0805 | Indole-3-acetate | 0.003238801 | 1.000000e+00 |
| B0901 | Staphyloferrin | 0.033797012 | 1.045425e-02 |
| B0902 | Aerobactin | 0.004016512 | 1.000000e+00 |
| B0903 | Staphylopine | 0.026547258 | 1.276233e-02 |
| B1004 | Bacilysin | -0.019592755 | 1.882566e-01 |
| B1012 | Fosfomycin | 0.041748103 | 1.506260e-03 |
| B1014 | Kanosamine | 0.003291927 | 1.000000e+00 |
| B1028 | Pyocyanin | 0.036245914 | 1.933005e-04 |
| D0101 | Triglyceride | 0.067359825 | 2.628573e-03 |
| D0102 | Fatty acid | 0.001114093 | 1.000000e+00 |
| D0103 | Oleate | 0.028341734 | 1.000000e+00 |
| D0104 | Dicarboxylic acids | -0.043831252 | 1.000000e+00 |
| D0201 | Cellulose | 0.139526853 | 1.172528e-03 |
| D0202 | Xyloglucan | 0.194107364 | 1.135739e-01 |
| D0203 | Starch | 0.217328224 | 1.000000e+00 |
| D0204 | Chitin | 0.056939483 | 1.000000e+00 |
| D0205 | Pectin | 0.166966707 | 2.387147e-02 |
| D0206 | Alpha galactan | 0.383968623 | 1.000000e+00 |
| D0207 | Beta-galactan | 0.347673216 | 9.566923e-01 |
| D0208 | Mixed-Linkage glucans | 0.182788325 | 5.967716e-01 |
| D0209 | Xylans | 0.268879339 | 1.047317e-02 |
| D0210 | Beta-mannan | 0.217084318 | 5.479793e-03 |
| D0211 | Alpha-mannan | 0.121559022 | 1.696668e-07 |
| D0212 | Arabinan | 0.358023402 | 4.330492e-05 |
| D0213 | Mucin | 0.271503069 | 2.839188e-01 |
| D0301 | Lactose | 0.022120411 | 2.001974e-01 |
| D0302 | Sucrose | 0.194515642 | 1.471257e-03 |
| D0303 | D-Apiose | 0.001448446 | 1.000000e+00 |
| D0304 | D-Arabinose | 0.143547948 | 1.000000e+00 |
| D0305 | D-Mannose | -0.092031194 | 1.471735e-02 |
| D0306 | D-Xylose | 0.246454359 | 1.097668e-04 |
| D0307 | L-Fucose | 0.196975665 | 9.266313e-03 |
| D0308 | L-Rhamnose | 0.213829078 | 1.000000e+00 |
| D0309 | Galactose | 0.113574961 | 1.000000e+00 |
| D0310 | NeuAc | 0.255990352 | 1.000000e+00 |
| D0501 | Serine | -0.247973804 | 3.812504e-03 |
| D0502 | Threonine | -0.210114768 | 1.000000e+00 |
| D0503 | Cysteine | 0.012739997 | 3.429585e-04 |
| D0504 | Methionine | 0.002898338 | 1.000000e+00 |
| D0505 | Valine | -0.126063939 | 1.000000e+00 |
| D0506 | Isoleucine | -0.067181509 | 5.267199e-03 |
| D0507 | Leucine | -0.011458718 | 1.000000e+00 |
| D0508 | Lysine | 0.032538573 | 8.166576e-05 |
| D0509 | Arginine | 0.009706886 | 1.000000e+00 |
| D0510 | Proline | 0.024264477 | 1.000000e+00 |
| D0511 | Glutamate | -0.101293585 | 1.000000e+00 |
| D0512 | Histidine | -0.125010734 | 1.000000e+00 |
| D0513 | Tryptophan | -0.304229107 | 1.000000e+00 |
| D0516 | Beta-alanine | -0.232368879 | 1.000000e+00 |
| D0517 | Ornithine | 0.009656190 | 3.304008e-01 |
| D0518 | GABA | 0.024186489 | 1.000000e+00 |
| D0601 | Nitrate | -0.046019486 | 1.000000e+00 |
| D0602 | Urea | 0.165501629 | 1.335954e-04 |
| D0603 | Urate | 0.005473487 | 1.439794e-01 |
| D0604 | GlcNAc | 0.458453390 | 1.254991e-02 |
| D0606 | Allantoin | 0.056328281 | 2.184103e-01 |
| D0607 | Creatinine | 0.035964568 | 1.431127e-02 |
| D0609 | L-carnitine | 0.140790141 | 1.643897e-04 |
| D0610 | Methylamine | -0.089224824 | 1.000000e+00 |
| D0611 | Phenylethylamine | 0.004795965 | 1.000000e+00 |
| D0612 | Hypotaurine | 0.014267712 | 1.000000e+00 |
| D0613 | Taurine | 0.096443326 | 1.000000e+00 |
| D0701 | 2,3-Butanediol | 0.003790326 | 1.000000e+00 |
| D0702 | Ethanol | -0.240044383 | 1.000000e+00 |
| D0704 | Glycerol | 0.083494880 | 1.000000e+00 |
| D0705 | Propylene glycol | -0.062393794 | 1.000000e+00 |
| D0706 | Ethylene glycol | -0.255591415 | 1.760625e-01 |
| D0708 | Phytol | -0.081903996 | 1.065901e-04 |
| D0801 | Toluene | 0.001551262 | 1.000000e+00 |
| D0802 | Xylene | 0.001551262 | 1.000000e+00 |
| D0805 | Benzoate | 0.001897626 | 1.000000e+00 |
| D0807 | Catechol | 0.023097664 | 1.000000e+00 |
| D0815 | Phthalate | 0.004042691 | 1.000000e+00 |
| D0816 | Phenylacetate | 0.038329639 | 1.000000e+00 |
| D0817 | Trans-cinnamate | 0.045829620 | 2.579984e-05 |
| D0901 | Penicillin | -0.182460165 | 1.000000e+00 |
| D0902 | Carbapenem | 0.037048290 | 1.279223e-02 |
| D0903 | Cephalosporin | 0.007544015 | 6.387796e-03 |
| D0904 | Oxacillin | 0.004385875 | 1.000000e+00 |
| D0905 | Streptogramin | -0.271876668 | 1.000000e+00 |
| D0907 | Tetracycline | 0.452642711 | 2.261808e-04 |
| D0908 | Macrolide | -0.160017386 | 1.000000e+00 |
| D0910 | Chloramphenicol | -0.093165710 | 1.000000e+00 |
| D0911 | Lincosamide | -0.260150907 | 1.000000e+00 |
| S0101 | Peptidoglycan | -0.180843448 | 4.554284e-08 |
| S0103 | Teichoic acid | -0.124792154 | 1.000000e+00 |
| S0104 | Lipoteichoic acid | 0.061887680 | 1.000000e+00 |
| S0105 | Lipopolysaccharide | 0.017904784 | 1.000000e+00 |
| S0201 | Flagellum | -0.198532641 | 1.000000e+00 |
| S0202 | Pilus | 0.053264508 | 1.561234e-04 |
| S0301 | Spore | -0.041956134 | 1.000000e+00 |