Oral Microbiome Metabarcoding in Two Invasive Small Mammals from New Zealand
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animal Ethics Statements
2.2. Sample Collection and Genomic Library Preparation
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Phylum | Family | Possum Specimens | Stoat Specimens | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
a | b | c | d | e | a | b | c | d | e | ||
Actinobacteria | Acidobacteriaceae | 2 | 0 | 0 | 9 | 6 | 0 | 0 | 0 | 0 | 0 |
C111 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | |
Actinomycetaceae | 6671 | 4399 | 6709 | 0 | 0 | 890 | 324 | 1155 | 238 | 4265 | |
Brevibacteriaceae | 5 | 7 | 0 | 11 | 7 | 0 | 0 | 0 | 0 | 0 | |
Cellulomonadaceae | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 4 | |
Corynebacteriaceae | 226 | 949 | 397 | 50 | 23 | 150 | 604 | 392 | 26 | 79 | |
Dermabacteraceae | 0 | 0 | 0 | 9 | 13 | 0 | 0 | 0 | 0 | 11 | |
Dermacoccaceae | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | |
Dietziaceae | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
Geodermatophilaceae | 0 | 0 | 0 | 0 | 7 | 0 | 0 | 0 | 0 | 0 | |
Intrasporangiaceae | 0 | 0 | 0 | 9 | 37 | 0 | 0 | 0 | 0 | 0 | |
Kineosporiaceae | 0 | 0 | 0 | 0 | 15 | 0 | 0 | 0 | 0 | 0 | |
Microbacteriaceae | 0 | 0 | 0 | 9 | 93 | 744 | 4 | 26 | 43 | 202 | |
Micrococcaceae | 26 | 18 | 0 | 5 | 36 | 0 | 65 | 90 | 1855 | 12 | |
Nakamurellaceae | 0 | 0 | 0 | 12 | 0 | 0 | 0 | 0 | 0 | 0 | |
Nocardioidaceae | 0 | 0 | 0 | 16 | 36 | 0 | 0 | 0 | 0 | 0 | |
Propionibacteriaceae | 6064 | 30 | 8846 | 123 | 42 | 113 | 6 | 257 | 120 | 115 | |
Pseudonocardiaceae | 0 | 0 | 0 | 3 | 17 | 0 | 0 | 0 | 0 | 0 | |
Sporichthyaceae | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | |
Streptomycetaceae | 0 | 0 | 0 | 4 | 29 | 0 | 0 | 3 | 0 | 0 | |
Williamsiaceae | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | |
Coriobacteriaceae | 0 | 2 | 9 | 0 | 6 | 0 | 9 | 0 | 2 | 0 | |
Euzebyaceae | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | |
Gaiellaceae | 0 | 0 | 0 | 2 | 3 | 0 | 0 | 0 | 0 | 0 | |
Patulibacteraceae | 0 | 0 | 0 | 0 | 14 | 0 | 0 | 0 | 0 | 0 | |
Solirubrobacteraceae | 0 | 0 | 0 | 7 | 11 | 0 | 0 | 0 | 0 | 0 | |
Bacteroidetes | Bacteroidaceae | 31 | 9 | 5 | 18 | 4 | 6 | 0 | 3 | 165 | 0 |
Porphyromonadaceae | 73 | 1286 | 42 | 29 | 20 | 3092 | 2093 | 466 | 482 | 5361 | |
Prevotellaceae | 38 | 63 | 53 | 35 | 91 | 156 | 572 | 62 | 157 | 494 | |
S24-7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 7 | 4 | |
Barnesiellaceae | 0 | 0 | 0 | 0 | 7 | 0 | 0 | 0 | 0 | 0 | |
Paraprevotellaceae | 3 | 9 | 0 | 0 | 7 | 4 | 0 | 0 | 6 | 0 | |
Cyclobacteriaceae | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
Cytophagaceae | 4 | 0 | 0 | 0 | 15 | 0 | 0 | 0 | 0 | 0 | |
Flavobacteriaceae | 4887 | 23,828 | 17,570 | 2099 | 17 | 2238 | 2809 | 937 | 1856 | 5121 | |
Weeksellaceae | 11,660 | 7945 | 2085 | 4249 | 14,979 | 405 | 945 | 477 | 111 | 1068 | |
Sphingobacteriaceae | 7 | 0 | 0 | 15 | 58 | 0 | 4 | 0 | 0 | 0 | |
Chitinophagaceae | 0 | 0 | 0 | 9 | 21 | 0 | 0 | 0 | 0 | 4 | |
Chloroflexi | Dolo_23 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 |
Firmicutes | Bacillaceae | 13 | 4 | 6 | 5 | 12 | 5 | 0 | 0 | 0 | 0 |
Paenibacillaceae | 0 | 0 | 0 | 0 | 0 | 5575 | 1657 | 0 | 2645 | 61 | |
Planococcaceae | 0 | 0 | 2 | 14 | 8 | 0 | 0 | 6 | 0 | 0 | |
Staphylococcaceae | 86 | 7 | 0 | 246 | 300 | 0 | 3 | 3 | 0 | 3 | |
Exiguobacteraceae | 0 | 4 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | |
Thermicanaceae | 5 | 0 | 0 | 4 | 9 | 0 | 0 | 0 | 0 | 0 | |
Gemellaceae | 10,310 | 1821 | 1049 | 12,727 | 15,233 | 3438 | 829 | 84 | 2015 | 0 | |
Aerococcaceae | 429 | 4295 | 218 | 1718 | 747 | 1226 | 4145 | 113 | 1258 | 1590 | |
Carnobacteriaceae | 10 | 11 | 5 | 2 | 46 | 80 | 7 | 11 | 130 | 98 | |
Enterococcaceae | 7 | 0 | 5 | 0 | 8 | 0 | 7 | 0 | 6 | 5 | |
Lactobacillaceae | 4 | 4 | 0 | 0 | 28 | 0 | 2 | 14 | 12 | 0 | |
Leuconostocaceae | 0 | 3 | 0 | 0 | 8 | 0 | 0 | 0 | 0 | 0 | |
Streptococcaceae | 51 | 840 | 132 | 3196 | 12,656 | 26,169 | 19,442 | 14,569 | 32,630 | 11,017 | |
Turicibacteraceae | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 14 | 0 | |
Clostridiaceae | 170 | 13 | 52 | 458 | 190 | 0 | 0 | 7 | 67 | 13 | |
Lachnospiraceae | 24 | 31 | 22 | 2 | 41 | 511 | 1153 | 175 | 814 | 191 | |
Peptococcaceae | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 9 | 0 | 4 | |
Peptostreptococcaceae | 37 | 6 | 0 | 166 | 53 | 0 | 28 | 26 | 0 | 2 | |
Ruminococcaceae | 20 | 12 | 6 | 7 | 42 | 4 | 5 | 0 | 0 | 34 | |
Veillonellaceae | 45 | 62 | 57 | 19 | 35 | 20 | 1666 | 97 | 454 | 57 | |
Acidaminobacteraceae | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 73 | 0 | 12 | |
Mogibacteriaceae | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 3 | |
Tissierellaceae | 45 | 0 | 7 | 9 | 6 | 4 | 0 | 15 | 0 | 8 | |
Erysipelotrichaceae | 0 | 1622 | 6 | 0 | 11 | 15 | 11 | 23 | 145 | 50 | |
Fusobacteria | Fusobacteriaceae | 21 | 20 | 19 | 54 | 66 | 5151 | 17,078 | 1478 | 7176 | 15,051 |
Leptotrichiaceae | 784 | 26 | 7 | 0 | 55 | 3050 | 28,266 | 2224 | 7229 | 17,960 | |
Proteobacteria | Caulobacteraceae | 6 | 0 | 0 | 5 | 10 | 0 | 0 | 0 | 0 | 0 |
Bradyrhizobiaceae | 0 | 0 | 0 | 9 | 0 | 0 | 0 | 0 | 0 | 0 | |
Brucellaceae | 0 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 | |
Hyphomicrobiaceae | 0 | 0 | 0 | 0 | 9 | 0 | 0 | 0 | 0 | 0 | |
Methylobacteriaceae | 0 | 0 | 0 | 14 | 72 | 0 | 0 | 0 | 0 | 0 | |
Methylocystaceae | 0 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 | |
Rhizobiaceae | 0 | 11 | 0 | 14 | 30 | 0 | 0 | 0 | 0 | 0 | |
Rhodobacteraceae | 0 | 0 | 0 | 3 | 11 | 0 | 0 | 0 | 0 | 4 | |
Acetobacteraceae | 5 | 0 | 2 | 0 | 29 | 0 | 0 | 0 | 0 | 0 | |
Rhodospirillaceae | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | |
mitochondria | 0 | 0 | 0 | 0 | 8 | 0 | 0 | 0 | 2 | 0 | |
Erythrobacteraceae | 0 | 0 | 0 | 0 | 8 | 0 | 0 | 0 | 0 | 0 | |
Sphingomonadaceae | 6 | 0 | 0 | 4 | 91 | 6 | 0 | 0 | 0 | 0 | |
Alcaligenaceae | 4 | 0 | 0 | 0 | 0 | 3 | 0 | 2 | 23 | 4 | |
Burkholderiaceae | 6992 | 29,794 | 1774 | 1606 | 66 | 1099 | 239 | 208 | 86 | 83 | |
Comamonadaceae | 2032 | 39 | 1616 | 7 | 56 | 99 | 0 | 40 | 14 | 158 | |
Oxalobacteraceae | 0 | 4 | 0 | 10 | 76 | 0 | 0 | 4 | 0 | 0 | |
Methylophilaceae | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
Neisseriaceae | 11,609 | 28,742 | 19,824 | 10,454 | 35,160 | 25,358 | 10,979 | 22,580 | 43,075 | 4938 | |
Rhodocyclaceae | 9 | 0 | 0 | 7 | 6 | 8 | 0 | 0 | 6 | 0 | |
Bdellovibrionaceae | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | |
Polyangiaceae | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
Syntrophobacteraceae | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | |
Campylobacteraceae | 3 | 0 | 0 | 0 | 11 | 71 | 54 | 19 | 29 | 55 | |
Helicobacteraceae | 71 | 4 | 95 | 128 | 3686 | 0 | 0 | 0 | 0 | 0 | |
Chromatiaceae | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
Cardiobacteriaceae | 3223 | 3521 | 6280 | 2 | 0 | 32 | 0 | 185 | 16 | 387 | |
Enterobacteriaceae | 41 | 40 | 24 | 35 | 140 | 0 | 0 | 0 | 0 | 0 | |
Halomonadaceae | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
Pasteurellaceae | 6193 | 9601 | 9533 | 5981 | 20,350 | 56,748 | 27,617 | 48,242 | 43,199 | 11,382 | |
Moraxellaceae | 8 | 0 | 0 | 66 | 281 | 1709 | 2623 | 588 | 298 | 59 | |
Pseudomonadaceae | 5 | 13 | 6 | 13 | 26 | 0 | 0 | 0 | 0 | 0 | |
Vibrionaceae | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 2 | 0 | 0 | |
Sinobacteraceae | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | |
Xanthomonadaceae | 16 | 3 | 0 | 26 | 77 | 2 | 0 | 0 | 0 | 0 | |
Spirochaetes | Spirochaetaceae | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 36 | 0 | 3 |
TM7 | F16 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 0 |
Tenericutes | Acholeplasmataceae | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 51 | 0 | 0 |
Anaeroplasmataceae | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | |
Mycoplasmataceae | 27,690 | 2951 | 13,142 | 4572 | 4017 | 0 | 4 | 14 | 0 | 0 | |
Thermotogae | Thermotogaceae | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
Thermi | Trueperaceae | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 |
Thermaceae | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Pathway | Possums | Stoats | ||
---|---|---|---|---|
Total | p-Values | Total | p-Values | |
Lipopolysaccharide biosynthesis | 17 | 0 | 17 | 0 |
Biosynthesis of amino acids | 222 | <0.001 | 222 | <0.001 |
Peptidoglycan biosynthesis | 13 | <0.001 | 13 | <0.001 |
Terpenoid backbone biosynthesis | 23 | <0.001 | 23 | <0.001 |
Streptomycin biosynthesis | 12 | <0.001 | 12 | <0.001 |
Polyketide sugar unit biosynthesis | 4 | <0.05 | 4 | <0.05 |
Valine, leucine and isoleucine biosynthesis | 15 | <0.05 | - | - |
Folate biosynthesis | 29 | <0.05 | - | - |
Porphyrin and chlorophyll metabolism | 69 | <0.001 | 69 | <0.001 |
Alanine, aspartate and glutamate metabolism | 62 | <0.001 | 62 | <0.001 |
Arginine and proline metabolism | 115 | <0.01 | 115 | <0.01 |
Cysteine and methionine metabolism | 71 | <0.01 | 71 | <0.01 |
Glycine, serine and threonine metabolism | 78 | <0.01 | 78 | <0.01 |
D-Glutamine and D-glutamate metabolism | 6 | <0.01 | 6 | <0.01 |
Thiamine metabolism | 23 | <0.01 | 23 | <0.01 |
Starch and sucrose metabolism | 65 | <0.01 | 65 | <0.05 |
Glyoxylate and dicarboxylate metabolism | 51 | <0.01 | 51 | <0.05 |
Biotin metabolism | 19 | <0.05 | 19 | <0.05 |
Riboflavin metabolism | 22 | <0.05 | 22 | <0.05 |
Amino sugar and nucleotide sugar metabolism | 64 | <0.05 | 64 | <0.05 |
Carbon metabolism | 249 | <0.05 | 249 | <0.05 |
Butanoate metabolism | 61 | <0.05 | - | - |
Nicotinate and nicotinamide metabolism | 36 | <0.05 | - | - |
beta-Alanine metabolism | - | - | 36 | <0.05 |
Vitamin B6 metabolism | - | - | 12 | <0.05 |
Phenylalanine metabolism | 41 | <0.05 | 41 | <0.01 |
Xylene degradation | 20 | <0.01 | 20 | <0.01 |
Steroid degradation | 9 | <0.05 | 9 | <0.05 |
Lysine degradation | - | - | 30 | <0.05 |
Synthesis and degradation of ketone bodies | 5 | <0.05 | 5 | <0.05 |
Pentose and glucuronate interconversions | 41 | <0.05 | 41 | <0,01 |
Carbon fixation in photosynthetic organisms | 35 | <0.05 | 35 | <0.05 |
Pentose phosphate pathway | - | - | 63 | <0.01 |
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Emami-Khoyi, A.; Benmazouz, I.; Paterson, A.M.; Ross, J.G.; Murphy, E.C.; Bothwell, J.; Alizadeh, H.; van Vuuren, B.J.; Teske, P.R. Oral Microbiome Metabarcoding in Two Invasive Small Mammals from New Zealand. Diversity 2020, 12, 278. https://doi.org/10.3390/d12070278
Emami-Khoyi A, Benmazouz I, Paterson AM, Ross JG, Murphy EC, Bothwell J, Alizadeh H, van Vuuren BJ, Teske PR. Oral Microbiome Metabarcoding in Two Invasive Small Mammals from New Zealand. Diversity. 2020; 12(7):278. https://doi.org/10.3390/d12070278
Chicago/Turabian StyleEmami-Khoyi, Arsalan, Isma Benmazouz, Adrian M. Paterson, James G. Ross, Elaine C. Murphy, Jennifer Bothwell, Hossein Alizadeh, Bettine Jansen van Vuuren, and Peter R. Teske. 2020. "Oral Microbiome Metabarcoding in Two Invasive Small Mammals from New Zealand" Diversity 12, no. 7: 278. https://doi.org/10.3390/d12070278
APA StyleEmami-Khoyi, A., Benmazouz, I., Paterson, A. M., Ross, J. G., Murphy, E. C., Bothwell, J., Alizadeh, H., van Vuuren, B. J., & Teske, P. R. (2020). Oral Microbiome Metabarcoding in Two Invasive Small Mammals from New Zealand. Diversity, 12(7), 278. https://doi.org/10.3390/d12070278