Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome

Rifkin, Riaan F.; Vikram, Surendra; Ramond, Jean-Baptiste; Rey-Iglesia, Alba; Brand, Tina B.; Porraz, Guillaume; Val, Aurore; Hall, Grant; Woodborne, Stephan; Le Bailly, Matthieu; Potgieter, Marnie; Underdown, Simon J.; Koopman, Jessica E.; Cowan, Don A.; Van de Peer, Yves; Willerslev, Eske; Hansen, Anders J.

doi:10.1186/s40168-020-00832-x

Table 2 DNA sequence reads for twelve authenticated pathogenic taxa detected in the BRS palaeo-faecal specimen

From: Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome

Phylum	Genus	Pathogenic clinical manifestations	E-LPC reads	BWA aligned (mapped) sequence reads						Mean read length (bp)	C-T p-value
Phylum	Genus	Pathogenic clinical manifestations	E-LPC reads	BRS1 SC1	BRS2	BRS3	BRS4	BRS5 SC2	Total	Mean read length (bp)	BRS1 SC1	BRS2	BRS3	BRS4	BRS5 SC2
Actinobacteria	Mycobacterium	Tuberculosis, leprosy, atypical infections	701	397	4535	1853	59096	487	67069	67.20	0.0707802	0.0017862	0.0037356	0.0100530	0.2953064
Bacteroidetes	Weeksella	Pneumonia, sepsis, peritonitis, urinary tract infections	1	0	461	175	2552	0	3189	45.40	−	0.0069370	0.0484237	0.1960360	−
Firmicutes	Listeria	Listeriosis (convulsions, septicaemia and meningitis)	0	92	453	233	5989	5	6772	72.80	0.0000005	0.3494000	0.0975000	0.8800000	−
Proteobacteria	Aeromonas	Gastroenteritis and wound infections	0	13	129	289	2033	29	2493	67.20	0.2264910	0.0206110	0.4139431	0.0060921	0.4998525
	Achromobacter	Skin, soft tissue and respiratory infections	21	150	36089	12869	160087	311	209527	72.40	0.0011408	0.0017379	0.0000094	0.0015504	0.1190260
	Bordetella	Pertussis (whooping cough, respiratory infection)	18	123	2027	683	16466	196	19513	69.60	0.0204611	0.1325985	0.0082522	0.0077918	0.2557714
	Burkholderia	Pulmonary infections (pneumonia, melioidosis)	12	48	869	287	6965	156	8337	62.00	0.2711432	0.0462580	0.2140947	0.3505477	0.1594083
	Comamonas	Acute appendicitis, urinary tract infection	8	79	3656	1467	40820	987	47017	73.40	0.6379285	0.0059303	0.0225115	0.0322217	0.6381353
	Delftia	Endocarditis, skin an ocular infections	226	594	921	348	10552	692	13333	74.80	0.2733595	0.0035008	0.5813131	0.0712462	0.0567663
	Lysobacter	Opportunistic pathogen, various symptoms	5	37	9616	3170	45813	95	58736	66.20	0.2478419	0.0013587	0.0003318	0.0064930	0.8210803
	Shigella	Shigellosis (dysentery, seizures, mucosal ulceration)	2	253	35046	12402	137623	762	186088	76.80	0.5381291	0.0002471	0.0000002	0.0002182	0.2954809
	Vibrio	Cholera (gastroenteritis, diarrhoea, septicaemia)	0	7	419	147	2333	21	2927	62.80	−	0.4420414	0.1131828	0.0005438	−
	*Total*		*994*	*1793*	*94221*	*33923*	*490329*	*3741*	*625001*	*67.55*	−	−	−	−

Statistically significant (i.e. verified ancient) C-T p values are indicated in bold text. BWA mapping was performed using high-quality filtered reads for DNA damage estimation analyses using PMDtools (‘C-T p values’) (see the ‘Methods’ section). Additional read-length information for individual taxa is provided in Table S5

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ISSN: 2049-2618

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