Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count

Figures & data

Demographics and clinical characteristics of participants

	Overall N = 36	CD4^+ T cells <300/mm^3N = 14	CD4^+ T cells >300/mm^3N = 22	P value^a
Age, years, median (IQR)	33 (29–40)	32 (29–38)	33 (29–44)	0.791^b
Male gender, N (%)	34 (94.4%)	13 (92.9%)	21 (95.5%)	0.715^c
Man who have sex with man, N (%)	30 (83.3%)	12 (85.7%)	18 (81.8%)	0.760^c
Baseline CD4^+ T cell/mm^3, median (IQR)	331 (247–429)	227 (150–263)	414 (345–484)	<0.001^b
Last visit CD4^+ T cell/mm^3, median (IQR)	467 (342–619)	370 (272–454)	581 (400–792)	0.001^d
Baseline CD4^+/CD8^+ ratio, %, median (IQR)	39.57 (25.33–39.57)	27.22 (14.48–42.49)	52.87 (32.12–67.93)	0.014^d
Last visit CD4^+/CD8^+ ratio, %, median (IQR)	63.12 (48.64–93.49)	55.30 (39.83–62.98)	89.45 (53.90–100.07)	0.005^d
Baseline HIV RNA lg10 copies/ml, median (IQR)	4.68 (4.18–5.12)	4.70 (4.25–5.41)	4.66 (3.62–5.08)	0.234^d
cART duration, months, median (IQR)	15 (14–16)	15 (14–16)	15 (14–17)	0.968^b

^aCompared between subjects with CD4⁺ T cells <300/mm³ and >300/mm³

^bAnalyzed by Mann–Whitney U test

^cAnalyzed by chi-square test

^dAnalyzed by t-test

Fig. 1 Differences in species α-diversity of fecal microbiota between HISs subgrouped by CD4⁺ T cell counts at 300/mm³.

a Shannon index: t test; b Simpson index: Mann–Whitney test

Fig. 2 Characterization of β-diversity of intestinal microbiota in HISs at baseline and follow-up by PCoA (the paired baseline and follow-up samples were connected with lines. a HISs with baseline CD4⁺ T cell counts <300/mm³; b HISs with baseline CD4⁺ T cell counts >300/mm³

Fig. 3 Paired comparisons (pairedttest) of α-diversity indices in HISs before and after cART treatment. a Analysis of the Shannon index in HISs with baseline CD4⁺ T cell counts <300/mm³; b Analysis of the Shannon index in HISs with baseline CD4⁺ T cell counts >300/mm³; c Analysis of the Simpson index in HISs with baseline CD4⁺ T cell counts <300/mm³; d Analysis of the Simpson index in HISs with baseline CD4⁺ T cell counts >300/mm³)

Fig. 4 The grouped microbial composition at the genus level at baseline and follow-up.

a HISs with baseline CD4⁺ T cell counts <300/mm³; b HISs with baseline CD4⁺ T cell counts >300/mm³

Alterations of gut microbiota composition in HIV positive participants with cART introduction

	Overall (N=36)				CD4+ T cell count <300/mm^3 (N=14)				CD4+ T cell count >300/mm^3 (N=22)
Change	Category	Taxonomy	LDA^a	P^b	Category	Taxonomy	LDA^a	P^b	Category	Taxonomy	LDA^a	P^b
Enrichment	Phylum	Fusobacteria	4.27	0.021	Order	Bacillales	4.06	0.001	Phylum	Fusobacteria	4.52	0.021
	Phylum	Proteobacteria	4.66	0.002	Family	Family_XII_o_Bacillales	4.05	<0.001	Phylum	Proteobacteria	4.77	0.005
	Class	Fusobacteriia	4.27	0.021	Genus	Exiguobacterium	4.05	<0.001	Class	Fusobacteriia	4.52	0.021
	Class	Gammaproteobacteria	4.67	0.003					Class	Gammaproteobacteria	4.78	0.004
	Order	Fusobacteriales	4.27	0.021					Order	Enterobacteriales	4.75	0.004
	Order	Enterobacteriales	4.60	0.008					Family	Enterobacteriaceae	4.75	0.004
	Family	Fusobacteriaceae	4.27	0.020					Genus	Klebsiella	4.09	0.001
	Family	Enterobacteriaceae	4.60	0.008
	Genus	Fusobacterium	4.27	0.017
	Genus	Klebsiella	4.12	<0.001
Depletion	Phylum	Bacteroidetes	4.78	0.027					Phylum	Bacteroidetes	4.97	0.010
	Class	Bacteroidia	4.78	0.027					Class	Bacteroidia	4.97	0.010
	Order	Bacteroidales	4.78	0.027					Order	Bacteroidales	4.97	0.010
	Family	Ruminococcaceae	4.63	0.006					Family	Ruminococcaceae	4.73	0.005
	Genus	Faecalibacterium	4.55	<0.001					Genus	Faecalibacterium	4.59	<0.001

^aAnalyzed by linear discriminant analysis effect size method

^bAnalyzed by paired Wilcoxon’s signed-rank test