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] |