A preliminary investigation on the relationship between gut microbiota and gene expressions in peripheral mononuclear cells of infants with autism spectrum disorders

Figures & data

Table 1. Relative abundance (%) of bacterial family/genera in the fecal microbiota of ASD infants and healthy infants.

Order	Family	Genus	Control (%)	ASD (%)
Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	13.74 ± 8.89	9.38 ± 5.38
Coriobacteriales	Coriobacteriaceae	Collinsella	<0.01	0.71 ± 1.58
Coriobacteriales	Coriobacteriaceae	Eggerthella	0.37 ± 0.17	0.14 ± 0.17
Bacteroidales	Bacteroidaceae	Bacteroides	18.64 ± 18.19	30.32 ± 8.21
Bacteroidales	Porphyromonadaceae	Parabacteroides	1.17 ± 1.47	1.46 ± 1.92
Bacteroidales	Rikenellaceae	Other	0.20 ± 0.50	1.71 ± 1.91
Bacteroidales	[Barnesiellaceae]	Other	<0.01	0.24 ± 0.39
Lactobacillales	Streptococcaceae	Lactococcus	0.08 ± 0.19	<0.01
Lactobacillales	Streptococcaceae	Streptococcus	6.36 ± 7.94	0.69 ± 0.55
Turicibacterales	Turicibacteraceae	Turicibacter	0.01 ± 0.02	0.09 ± 0.12
Clostridiales	Other	Other	<0.01	0.10 ± 0.17
Clostridiales	Christensenellaceae	Other	<0.01	0.03 ± 0.09
Clostridiales	Clostridiaceae	Other	0.32 ± 0.56	0.04±0.08
Clostridiales	Clostridiaceae	Clostridium	1.83 ± 1.96	1.44 ± 1.64
Clostridiales	Clostridiaceae	SMB53	0.17 ± 0.31	<0.01
Clostridiales	Lachnospiraceae	Other	6.28 ± 3.38	3.05 ± 1.93
Clostridiales	Lachnospiraceae	Anaerostipes	0.03 ± 0.05	0.40 ± 0.62
Clostridiales	Lachnospiraceae	Blautia	14.21 ± 10.02	3.34 ± 4.50
Clostridiales	Lachnospiraceae	Coprococcus	3.08 ± 2.41	1.17 ± 0.92
Clostridiales	Lachnospiraceae	Dorea	1.07 ± 0.90	1.26 ± 1.72
Clostridiales	Lachnospiraceae	Lachnospira	0.13 ± 0.23	0.26 ± 0.41
Clostridiales	Lachnospiraceae	Roseburia	2.01 ± 3.84	4.68 ± 4.92
Clostridiales	Lachnospiraceae	[Ruminococcus]	5.54 ± 4.41	2.59 ± 2.78
Clostridiales	Peptostreptococcaceae	Other	0.59 ± 0.90	0.36 ± 0.10
Clostridiales	Ruminococcaceae	Other	7.69 ± 6.85	4.84 ± 5.01
Clostridiales	Ruminococcaceae	Anaerotruncus	0.06 ± 0.07	0.07 ± 0.11
Clostridiales	Ruminococcaceae	Faecalibacterium	3.25 ± 1.61	9.78 ± 6.75
Clostridiales	Ruminococcaceae	Oscillospira	0.41 ± 0.36	1.36 ± 1.64
Clostridiales	Ruminococcaceae	Ruminococcus	2.29 ± 2.43	2.94 ± 1.79
Clostridiales	Veillonellaceae	Acidaminococcus	<0.01	0.12 ± 0.30
Clostridiales	Veillonellaceae	Dialister	0.81 ± 1.22	0.49 ± 0.49
Clostridiales	Veillonellaceae	Megamonas	<0.01	0.98 ± 2.41
Clostridiales	Veillonellaceae	Megasphaera	0.03 ± 0.07	0.36 ± 0.55
Clostridiales	Veillonellaceae	Phascolarctobacterium	<0.01	0.15 ± 0.37
Clostridiales	Veillonellaceae	Veillonella	3.58 ± 2.75	4.28 ± 5.50
Clostridiales	[Mogibacteriaceae]	Other	0.17 ± 0.27	0.03 ± 0.04
Erysipelotrichales	Erysipelotrichaceae	Other	1.92 ± 1.68	0.72 ± 0.90
Erysipelotrichales	Erysipelotrichaceae	Coprobacillus	0.02 ± 0.06	<0.01
Erysipelotrichales	Erysipelotrichaceae	[Eubacterium]	0.47 ± 0.26	0.19 ± 0.23
Burkholderiales	Alcaligenaceae	Sutterella	0.01 ± 0.01	0.98 ± 2.03
Desulfovibrionales	Desulfovibrionaceae	Bilophila	<0.01	0.05 ± 0.09
Desulfovibrionales	Desulfovibrionaceae	Desulfovibrio	0.02 ± 0.04	0.05 ± 0.13
Enterobacteriales	Enterobacteriaceae	Other	0.22 ± 0.20	1.14 ± 1.52
Enterobacteriales	Enterobacteriaceae	Klebsiella	0.67 ± 1.64	0.01 ± 0.01
Verrucomicrobiales	Verrucomicrobiaceae	Akkermansia	2.57 ± 6.22	7.96 ± 5.53

Notes: Data are presented as mean ± SD. Bold text indicates that taxa are significantly different between ASD infants and healthy infants (p < 0.05).

Table 2. GO pathways enriched for the differentially expressed genes between ASD infants and healthy infants.

ID	Pathway name	significance*	Total genes**	p value
GO:0009615	Response to virus	27	296	9.E-06
GO:0051607	Defense response to virus	21	199	1.E-05
GO:0006952	Defense response	75	1412	3.E-04
GO:0050688	Regulation of defense response to virus	10	77	4.E-04
GO:0046456	Icosanoid biosynthetic process	8	51	4.E-04
GO:1901570	Fatty acid derivative biosynthetic process	8	51	4.E-04
GO:0045071	Negative regulation of viral genome replication	7	40	5.E-04
GO:0009954	Proximal/distal pattern formation	6	30	6.E-04
GO:0006826	Iron ion transport	8	54	6.E-04
GO:0098542	Defense response to other organism	26	365	7.E-04
GO:0006636	Unsaturated fatty acid biosynthetic process	8	59	1.E-03
GO:0019050	Suppression by virus of host apoptotic process	2	2	1.E-03
GO:0033668	Negative regulation by symbiont of host apoptotic process	2	2	1.E-03
GO:0039526	Modulation by virus of host apoptotic process	2	2	1.E-03
GO:0052041	Negative regulation by symbiont of host programmed cell death	2	2	1.E-03
GO:0052490	Negative regulation by organism of programmed cell death in other
	Organism involved in symbiotic interaction	2	2	1.E-03
GO:0061324	Canonical Wnt signalling pathway involved in positive regulation of
	Cardiac outflow tract cell proliferation	2	2	1.E-03
GO:1901963	Regulation of cell proliferation involved in outflow tract morphogenesis	2	2	1.E-03
GO:0060548	Negative regulation of cell death	43	721	1.E-03
GO:0048525	Negative regulation of viral process	9	75	1.E-03

Note: Only the top 20 pathways are shown.

^* Significance (p < 0.05) was calculated by comparing the number of differentially expressed genes between groups.

^** Total number of genes assigned to each pathway. Differentially expressed genes were imported into iPathway software.

Table 3. Interferon-related GO pathways enriched for the differentially expressed genes between ASD infants and healthy infants.

ID	Pathway name	Significance*	Total genes**	p value
GO:0034341	Response to interferon-gamma	11	117	0.003
GO:0060333	Interferon-gamma-mediated signaling pathway	8	74	0.005
GO:0071346	Cellular response to interferon-gamma	9	97	0.008
GO:0045351	Type I interferon biosynthetic process	3	13	0.01
GO:0060337	Type I interferon signaling pathway	7	73	0.016
GO:0071357	Cellular response to type I interferon	7	73	0.016
GO:0034340	Response to type I interferon	7	74	0.017
GO:0035456	Response to interferon-beta	3	18	0.025

^* Significance (p < 0.05) was calculated by comparing the number of differentially expressed genes between groups.

^** Total number of genes assigned to each pathway. Differentially expressed genes were imported into iPathway software.

Table 4. Correlation between the expression level of genes involved in interferon signaling pathways in PBMC and the abundance of Faecalibacterium and Blautia in fecal microbiota.

GO process		Interferon gamma mediated signalling pathway (GO:0060333)
Genes		IRF7	IRF9	SP100	HLA-DQA1	HLA-DQB1	CAMK2G	HCK	PML
Fold difference (vs. healthy infants)		3.38	1.81	1.94	−1.68	−2.17	−1.92	−2.56	2.50
Correlation (r) §	Faecalibacterium	0.76*	0.75*	0.43	−0.61	−0.63†	−0.71†	−0.67†	0.74*
	Blautia	0.84†	−0.29	−0.67†	0.81*	0.67†	0.55	0.64†	−0.42
GO process		Type I interferon signalling pathway (GO:0060337)
Genes		IRF7	IRF9	SP100	IFITM1	IFIT1	ISG20	MX1
Fold difference (vs. healthy infants)		3.38	1.81	1.94	1.99	10.23	3.68	5.42
Correlation (r) §	Faecalibacterium	0.76*	0.75*	0.43	0.80*	0.80*	0.82*	0.74*
	Blautia	−0.84†	−0.29	−0.67†	−0.58	−0.48	−0.49	−0.64†

Notes: Fold differences of the differentially expressed genes between groups involved in GO:0060333 and GO:0060337 are shown. §Pearson’s r between gene expression levels in PBMC and the fecal abundance of Faecalibacterium or Blautia was calculated by R.

^* p < 0.05.

^† p < 0.1.

Fig. 1. Correlation of gene expression levels in PBMC with the abundance of genus Faecalibacterium in fecal microbiota.

Notes: Gene expression levels of IRF7 (A), IRF9 (B), CXCL10 (C) and CXCL11 (D) in healthy infants (squares) and ASD infants (triangles) were assessed by real-time PCR and their correlation with the abundance of Faecalibacterium in fecal microbiota evaluated. Correlations (r) and statistical significance were determined by Pearson’s product-moment correlation. The correlation (r) and P values are shown in the figure.