Gut microbiome time series during cephalosporin exposure

OBJECTIVE: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species. DESIGN: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria. RESULTS: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, U Borkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals. CONCLUSION: The bloom of U B. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.

• host run.scientific_name · “human gut metagenome”
• body site study.title · “Metagenomic stool samples”
• life stage study.description · “healthy human adult gut microbiome”

29 runs over 17 samples · mean 4.88 Gbp per run (median 5.07 Gbp, total 141.39 Gbp; 29 runs with a base count) · layout PAIRED 29 · platform ILLUMINA 29 · models Illumina HiSeq 2000 (20), Illumina HiSeq 4000 (8), Illumina MiSeq (1) · 93% of runs with a Sandpiper profile · first public 2019-03-14

Hildebrand F first · Moitinho-Silva L · Blasche S · Jahn MT · Gossmann TI · Huerta-Cepas J · Hercog R · Luetge M · Bahram M · Pryszlak A · Alves RJ · Waszak SM · Zhu A · Ye L · Costea PI · Aalvink S · Belzer C · Forslund SK · Sunagawa S · Hentschel U · Merten C · Patil KR · Benes V · Bork P last

PRJEB28730.csv.gz (1.5 KB) · parquet (71.5 KB) — all 17 samples, every field with route and confidence · PRJEB28730_determinations.csv.gz (2.2 KB) — 178 evidence rows