Table 1.
Results of studies that address the effects of antibiotic treatment on the human gut microbiota.
| Short Term Effectsb | Long Term Effectsc | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Divd | Come | Taxaf | ABRg | Divd | Compc | Taxaf | ABRg | ||||||||
| Reference | Treatment Mechanisma | ACT | BAC | FIR | PRO | ACT | BAC | FIR | PRO | ||||||
| (De La Cochetière et al. 2005) | Cell Wall Synthesis Inhibitor | D | — | — | ↑(2u) | ↑(1u) | ∼D | — | — | — | — | ||||
| (Jernberg et al. 2007) | Protein Synthesis Inhibitor | ↓* | D* | ↑ | ↓h | Dh | ↑ | ||||||||
| (Dethlefsen et al. 2008) | DNA Synthesis Inhibitor | ↓* | D | |*(8u) | |*(72u) | |*(335u) | |*(8u) | — | — | — | |*(4u) | |*(39u) | |*(2u) | ||
| (Jakobsson et al. 2010) | DNA Inhibitor and Protein Synthesis Inhibitor | ↓ | D | ↓(p, 2g) | — | ↑(1g)↓(1g) | — | ↑ | — | ∼D | — | — | — | — | ↑ |
| (Dethlefsen and Relman 2011) | DNA Synthesis Inhibitor | ↓* | D | — | ↑(≥4u)↓(≥13u) | ↑(≥7u)↓(≥8u) | ↓(≥2u) | ↑ | — | D* | — | — | — | — | — |
| (Morotomi et al. 2011) | Cell Wall Synthesis Inhibitor or Protein Synthesis Inhibitor | D | — | ↑(1g) | ↑(2g) | — | — | — | — | — | — | ||||
| (Bajaj et al. 2013) | RNA Synthesis Inhibitor | ∼D* | — | — | ↑*(1f)↓*(1f) | — | |||||||||
| (O'Sullivan et al. 2013) | Various | ∼↓ | — | |*(1g)↓*(1g) | ↑*(p) | |*(1f, 5g)↑*(8g)↓*(p, 1f, 5g) | |*(1g)↑*(1f, 1g)↓*(p) | ||||||||
| (Pérez-Cobas et al. 2013b) | Cell Wall Synthesis Inhibitor | ↓ | D | — | ↑(6u) | ↑(1u)↓(4u) | — | ∼↑ | — | — | ↓(2g) | ↓(1g) | ↓(4g) | ↓(1g) | — |
| (Arat et al., 2015) | Targets Bacterial Peptide Deformylase | ↓ | D | ↑*(3u) | ↓*(5u) | ↑*(1u)↓*(7u) | ↑*(2u) | ↑* | |||||||
| (Ladirat et al. 2014) | Cell Wall Synthesis Inhibitor | ↓*(1g) | ↑*(1u) | ↓*(14-22u) | ↑*(5u) | — | |(1g) | — | — | ||||||
| (Panda et al., 2014) | Various | ↓* | D | — | ↑*(p, 1c, 1o, 1g, ≥12u) | ↑*(2u)↓*(p, 1u) | — | ||||||||
| (Abeles et al. 2015) | Various | ↓* | ∼D | — | ∼↓(p) | ∼↑(p) | — | ↑ | |||||||
| (Heinsen et al. 2015) | Protein Synthesis Inhibitor | ↓* | D* | — | — | ↑*(1u)↓*(22u) | ↑*(1u) | — | D* | — | — | ↓*(3u) | — | ||
| (Rashid et al. 2015) | DNA Synthesis Inhibitor or Protein Synthesis Inhibitor | ↓* | ↓(1t) | ↑*(1g) | ↓*(1g)↓(2t) | ↓(1s) | —i | —i | —i | —i | —i | ||||
| (Stewardson et al., 2015) | Various | ∼↓ | D* | ↓*(p, 1c, 1o, 1f, 1g) | ↑*(p, 1c, 1o, 1f, 1g, 1u)↓*(2f, 2g, 2u) | ↑*(1f, 4g, 5u)↓*(2f, 2g, 10u)↕*(1g, 1u) | — | — | D* | ↕*(p, 1c) | ↓*(2f, 2g, 5u) | ↑*(1c, 1f, 1g, 5u)↓*(2g, 2u) | — | ||
| (Willmann et al. 2015) | DNA Synthesis Inhibitor | ∼↓ | D | — | — | — | ↓(p) | D | — | ∼D | — | — | — | — | ∼D |
| (Zaura et al. 2015) | Various | ↓* | D* | — | ↑*(1g) | ↓*(3g) | ↓*(1g) | — | ↓* | — | — | — | — | — | |
| (Raymond et al. 2016) | Cell Wall Synthesis Inhibitor | ∼↓ | ↓*(1c, 2f, 3g, 8s) | ↑*(1g, 1s)↓*(7s) | ↑*(2g, 8s)↓*(1c, 2f, 11g, 23s, 2ss) | ↓*(2f, 3g, 2s) | ↑* | — | ↓*(1f, 1g) | — | ↓*(1f, 3s) | ↓*(1f) | — | ||
| (Wipperman et al. 2017) | Combination | ↓* | D* | ↓(1g) | ↑(1g) | ↑(1g)↓(4g) | — | ↑* | ∼D* | — | ↑(1g)↓(1g) | ↑(3g, 1s) | ↑(1g, 1s) | ||
| (MacPherson et al. 2018) | Cell Wall Synthesis Inhibitor | ↓* | D | ↑*(1u)↓*(3u) | ↑*(5u) | ↑*(24u)↓*(95u) | ↑*(1f, 3u) | ↑* | — | — | — | — | ↑(3u) | — | — |
| (Suez et al. 2018) | DNA Synthesis Inhibitor and DNA Inhibitor | ↓* | D* | ↑*(3g)↓*(1g) | ↓*(5g, 6s) | ↑*(6g, 4s)↓*(9g, 8s) | ↑*(1g)↓*(1g) | — i | D* | ||||||
| (Dubinsky et al. 2020) | DNA Synthesis Inhibitor and/or DNA Inhibitor | ↓* | D* | ↑*(3u)↓*(10u) | ↑*(1u)↓*(12u) | ↑*(10u)↓*(45u) | ↑*(6u)↓*(4u) | ↑* | |||||||
Any effect shown within any subset of data within a study is presented here; for a more detailed summary, see Supplementary Table 1. ‘↑’ Indicates a positive effect on a variable, ‘↓’ indicates a negative effect on a variable, ‘|’ indicates a demonstrated effect of unclear direction, ‘↕’ indicates both a positive and negative effect shown according to different treatments or measurements, and ‘∼’ indicates a ‘possible’ or ‘slight’ effect. ‘D’ indicates clear disturbance of composition from baseline conditions or a control group. A blank space indicates that a variable was not measured by that study, and '—' indicates that the variable was measured, but no effect was found. Any entry in bold, with an asterisk ‘*’ was judged as significant by the authors of the study in question.
‘Treatment Mechanism’ column shows the mode of action of the antibiotic used in the study.
‘Short Term Effects’ columns show effects during, or immediately following, antibiotic treatment.
‘Long Term Effects’ columns show effects ranging between 14–1460 days after treatment ends.
‘Div’ columns show the effects on the diversity of the samples, according to metrics such as richness, Shannon Index, and Simpson Index
‘Com’ columns show the effects on the community composition of the samples, summarised by methods such as Bray-Curtis Dissimilarity, UniFrac Distances, and Principal Component Analysis.
‘Taxa’ columns show the effects on specific taxa in the in the samples, split into columns for each major phyla (ACT: Actinobacteria, BAC: Bacteroidetes, FIR: Firmicutes, and PRO: Proteobacteria), and listed following the codes: ‘t’ unclear taxa, ‘p’ phylum, ‘c’ class, ‘o’ order, ‘f’ family, ‘g’ genus, ‘s’ species, ‘ss’ subspecies and ‘u’ Operational Taxonomic Unit (OTU). The identities of taxa were confirmed using the List of Prokaryotic Names with Standing in Nomenclature (Parte 2018).
‘ABR’ columns show the effects on antibiotic resistance phenotypes or genes in samples.
Result specifically for Bacteroides species.
Results showing no clear effect were found at the end of study, but meaningful effects were measured at previous time points that would also be considered ‘long term’ as detailed in Table S1 (Supporting Information).