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Table 1 Summary table of research detailing the effect of co-infections on the level of dysbiosis in host guts

From: A framework for testing the impact of co-infections on host gut microbiomes

Host

Reference-infectant

Co-infectant

Level of dysbiosis

Taxa abundance

α-diversity

Impact

ß-diversity

Impact

References

Veterinary research

Domestic pig (Sus scrofa domesticus)

Bacterium (Salmonella enterica serovar Typhimurium)

Bacterium (Lawsonia intracellularis)

↓ Clostridium

↑ Lactobacillus

 ~Evenness (Simpson), richness (Chao1, ASVs)

N, A

Homogeneous clustering

A

[48]

Domestic chicken (Gallus gallus domesticus)

Protozoan (Histomonas meleagridis)

Bacterium (Avian pathogenic E. coli)

↓ Lactobacillus, Faecalibacterium, Ruminococcaceae;

↑ Escherichia, Bacteroides, Fusobacterium, Helicobacter

↓ Richness (Chao1) and diversity (Shannon)

S

↑ Heterogeneous clustering

S

[49]

Domestic chicken (G. gallus domesticus)

Virus (Avian leukosis virus-J)

Virus (Marek’s disease virus; Avian reticuloendotheliosis virus)

↑ Bacteroides, Enterococcus

↑ Richness (Chao1);

 ~ Diversity* (Shannon)

S

↑ Heterogeneous clustering

S

[50]

Experimental laboratory research

Lab mouse (Mus musculus—INS-GAS)

Helminth (Heligmosomoides polygyrus)

Bacterium (Helicobacter pylori)

↓ colonisation of Altered Schaedler Flora 356

Na

Na

na

na

[51]

Lab mouse (M. musculus—C57BL/6 WT Stat6±)

Helminth (Trichinella spiralis)

Virus (murine norovirus MNV CW3)

↓ Turicibacteraceae;

↑ Lactobacillacaeae, Clostridiales

Na

Na

na

na

[52]

Lab mouse (M. musculus—C57B1/6)

Protozoan (Giardia lamblia)

Bacterium (E. coli)

↑ Enterobacteriaceae

Na

Na

na

na

[53]

Lab mouse (M. musculus—C57BL/6)

Bacterium (Campylobacter jejuni)

Protozoan (Toxoplasma gondii), Bacteria (S. typhimurium; entero-invasive E. coli; Listeria monocytogenes)

↑ Enterobacteriaceae in C. jejuni/T. gondii and C. jejuni/S. typhimurium coinfected mice;

↓ Clostridiales and Lachnospiraceae in all co-infected groups; ↑ Dorea and unclassified S24-7 in C. jejuni/E. coli

 ~ /↓ Richness (Chao1) and diversity (Shannon)

N, A

na

na

[54]

Lab mouse (M. musculus—SPF ICR)

Protozoan (T. gondii)

Helminth (Schistosoma japonicum)

↑ Clostridiaceae

↓ Richness (Chao1);

 ~ diversity (Shannon);

S

↑ Heterogeneous clustering

S

[55]

Medical research

Human (Homo sapiens)

Norovirus (NV)

Bacteria (Enterotoxigenic E. coli)

↑ Bacteroides

 ~ Richness (Chao1), evenness (Simpson)

N

↑ Heterogeneous clustering than single infections

N

[56]

Human (Homo sapiens)

Norovirus (NV) or Rotavirus (RV)

Bacteria (Enteroaggregative or enteropathogenic E. coli)

↓ Enterococcus and Veillonellaceae in NV-E. coli co-infected; In RV infected, Lachnospiraceae and Collinsella were differentially abundant dep. on E. coli co-infectant

 ~ Diversity (Shannon) for NV-co-infected; ↓ diversity only for RV + EAEC

N, S

na

na

[57]

Human (H. sapiens)

Protozoan (Plasmodium vivax)

Helminths (e.g., Trichuris trichiura)

↓ Bacteroides; ↑ Prevotella copri, Clostridiaceae

 ~ Diversity (Shannon)

N

Homogeneous clustering

N, A

[58]

Human (H. sapiens)

Eukaryote (Giardia duodenalis)

Helminths (e.g., Ascaris lumbricoides)

↑ Prevotella (e.g., Prevotella copri) compared with helminth single infected group

 ~ Diversity (Shannon) to uninfected, but ↑ than G. duodenalis and ↓ than helminth singly-infected

A

na

na

[59]

Human (H. sapiens)

Virus (Human immunodeficiency virus)

Virus (Hepatitis C virus)

-

↓ Diversity (Shannon)

S

↑ ß-diversity distances

S

[60]

Wildlife research

African buffalo (Syncerus caffer)

Bacterium (Mycobacterium bovis)

Nematodes (e.g., Cooperia fuelleborni)

↓ SHD-231

 ~ Diversity (Shannon), evenness (Pielou), OTU richness

N

 ~ ß-diversity distances

N

[61]

  1. The identity of the host and co-infecting parasite species is shown in relation to the impacts reported, starting with changes in taxa abundance, α-diversity and ß-diversity. Diversity metrices were assessed based on the nature of change seen following co-infection (i.e., neutral, synergistic, antagonistic) in relation to the effect observed after a single infection (with the reference infectant). Details on the literature survey and references are provided in the Additional file, Additional file 1: Fig. S1, Table S1)
  2. na signifies a lack of information; impacts: N = neutral, S = synergistic, A = antagonistic; ↑ = increase; ↓ = decrease; ~  = comparable with single infection unless otherwise specified