Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials
2.2. Experimental Design and Bioreactor System
2.3. Sample Collection and Storage
2.4. Analytical Tests
2.5. DNA Sequencing and Metagenome Assembly
2.6. Microbial Community Analysis
2.7. Machine Learning Functional Classifications
2.8. Gene and Metabolic Pathway Predictions
2.9. Phylogenetic Tree Generation
3. Results
3.1. Microbial Fermentation of Dairy Coproduct Mixtures
3.2. Metagenomic Analysis of Bioreactor Microbial Communities
3.3. Lactic Acid Pathway Analysis
4. Discussion
4.1. Communities Enriched for Lactic Acid Producing Organisms
4.2. The Presence of Chain Elongators Were Associated with Lower Lactic Acid Accumulation
4.3. Communities Exhibited a High Degree of Functional Redundancy
4.4. Current Questions of Pathway Utilization
4.5. Comparison to UFMP-Fed Bioreactor
4.6. Concluding Remarks
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Characteristic | Value a |
---|---|
Total chemical oxygen demand (g COD/L) | 63 ± 2 (n = 4) |
Soluble chemical oxygen demand (g COD/L) | 64 ± 2 (n = 4) |
Lactose (g COD/L) | 52 ± 3 (n = 4) |
Lactic acid (g COD/L) | 3 ± 0 (n = 4) |
Total soluble protein (g COD/L) b | 4 ± 0 (n = 5) |
Total nitrogen (mg/L) | 680 ± 10 (n = 5) |
pH | 4.93 ± 0.02 (n = 3) |
MAG ID | Phylum a | Classification a | Reference Genome a | ANI a | Quality b | Completeness c (%) | Contamination c (%) | MAG Size c (bp) | Contigs c | N50 c (bp) | %GC c | NCBI Genome Accession Number | Reactor of Origin d |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ATO1 | Actinomycetota | Tractidigestivibacter scatoligenes | GCF_001494635.1 | 0.9565 | MQ | 98.39 | 0 | 2,241,335 | 40 | 140,862 | 62.75 | GCA_036454705.1 | A2 |
ATO2 | Actinomycetota | UBA7741 | N/A | N/A | MQ | 98.39 | 0.27 | 2,092,240 | 63 | 45,270 | 69.72 | GCA_036454645.1 | S2 |
ATO3 | Actinomycetota | UBA7748 sp900314535 | GCA_900314535.1 | 0.9723 | MQ | 95.97 | 0.81 | 2,022,229 | 69 | 34,988 | 60.23 | GCA_036454665.1 | B1 |
ATO4 | Actinomycetota | Olegusella sp002407925 | GCA_002407925.1 | 0.9865 | MQ | 80.65 | 0 | 1,498,345 | 8 | 252,912 | 55.53 | GCA_036454505.1 | A1 |
COR1 | Actinomycetota | CAIFEU01 sp903789505 | GCA_903789505.1 | 0.9735 | MQ | 95.16 | 1.41 | 2,881,083 | 38 | 127,573 | 69.49 | GCA_036453905.1 | S1 |
EGG1 | Actinomycetota | CAIFEB01 sp903789375 | GCA_903789375.1 | 0.9674 | MQ | 97.9 | 0 | 2,264,117 | 63 | 44,458 | 64.89 | GCA_036453845.1 | S2 |
BIF1 | Actinomycetota | Bifidobacterium mongoliense | GCF_000741285.1 | 0.9757 | MQ | 99.73 | 1.14 | 2,108,758 | 7 | 1,311,668 | 63.18 | GCA_036454425.1 | B3 |
BIF2 | Actinomycetota | Bifidobacterium crudilactis | GCF_000738005.1 | 0.9749 | HQ | 99.08 | 2.12 | 2,461,645 | 7 | 508,638 | 57.61 | GCA_036454125.1 | B3 |
BIF3 | Actinomycetota | Bifidobacterium subtile | GCF_000741775.1 | 0.9894 | MQ | 99.44 | 2.73 | 2,748,131 | 16 | 283,464 | 61.21 | GCA_036454005.1 | B1 |
BIF4 | Actinomycetota | Bifidobacterium thermophilum | GCA_000771265.1 | 0.9551 | MQ | 100 | 0.15 | 2,049,272 | 27 | 111,917 | 60.52 | GCA_036453945.1 | A2 |
BIF5 | Actinomycetota | Bifidobacterium sp022649135 | GCA_022649135.1 | 0.9934 | MQ | 98.31 | 1.53 | 2,450,011 | 41 | 95,366 | 61.5 | GCA_036453965.1 | A1 |
PROP1 | Actinomycetota | Acidipropionibacterium acidipropionici | GCF_001441165.1 | 0.9883 | MQ | 100 | 0 | 3,480,401 | 29 | 187,533 | 68.94 | GCA_036452805.1 | A3 |
LAC1 | Bacillota | Lactobacillus delbrueckii | GCF_001433875.1 | 0.9759 | MQ | 95.78 | 0 | 1,796,983 | 54 | 45,732 | 50.08 | GCA_036453405.1 | A1 |
LAC2 | Bacillota | Lactobacillus absiana | GCA_017309015.1 | 0.9782 | MQ | 79.99 | 0.97 | 1,391,865 | 75 | 19,352 | 52.73 | GCA_036455685.1 | A1 |
LAC3 | Bacillota | Lactobacillus amylovorus | GCF_002706375.1 | 0.9756 | MQ | 79.28 | 0.09 | 1,343,105 | 73 | 21,953 | 38.61 | GCA_036453345.1 | A1 |
LACCAS1 | Bacillota | Lacticaseibacillus paracasei | GCF_000829035.1 | 0.9836 | HQ | 99.46 | 0 | 2,787,648 | 39 | 102,065 | 46.5 | GCA_036453305.1 | A3 |
LACCAS2 | Bacillota | Lacticaseibacillus rhamnosus | GCF_900636965.1 | 0.9749 | MQ | 80.98 | 0 | 2,071,044 | 23 | 132,814 | 46.82 | GCA_036453285.1 | B1 |
LEUC1 | Bacillota | Leuconostoc gelidum | GCF_000166715.1 | 0.9875 | MQ | 99.44 | 0.19 | 1,870,646 | 8 | 442,939 | 36.63 | GCA_036453045.1 | B2 |
LEUC2 | Bacillota | Leuconostoc mesenteroides | GCF_000014445.1 | 0.9903 | MQ | 100 | 0 | 1,800,527 | 24 | 92,862 | 37.7 | GCA_036452885.1 | A2 |
LENLAC1 | Bacillota | Lentilactobacillus sunkii | GCF_001435575.1 | 0.966 | MQ | 98.89 | 0 | 2,748,557 | 25 | 142,530 | 42.13 | GCA_036453105.1 | B1 |
STREP1 | Bacillota | Lactococcus lactis | GCF_900099625.1 | 0.9846 | MQ | 100 | 0.28 | 2,510,060 | 20 | 233,864 | 34.87 | GCA_036452675.1 | A2 |
STREP2 | Bacillota | Lactococcus cremoris | GCF_001591705.1 | 0.9826 | MQ | 85.85 | 0.38 | 1,744,274 | 56 | 36,778 | 35.7 | GCA_036452495.1 | B1 |
BACIL1 | Bacillota | Weizmannia coagulans | GCF_000290615.1 | 0.9832 | MQ | 91.61 | 0 | 2,447,334 | 70 | 48,544 | 47.87 | GCA_036454485.1 | B2 |
ERY1 | Bacillota | Bulleidia | N/A | N/A | MQ | 96.19 | 0.45 | 2,113,669 | 59 | 50,393 | 47.89 | GCA_036453465.1 | A2 |
ERY2 | Bacillota | Bulleidia sp900319505 | GCA_900319505.1 | 0.9523 | MQ | 92.52 | 0.32 | 1,691,123 | 66 | 30,478 | 47.86 | GCA_036453425.1 | S1 |
LCO1 | Bacillota A | Bilifractor sp900319355 | GCA_900319355.1 | 0.9934 | MQ | 97.13 | 0.32 | 2,309,795 | 40 | 80,513 | 52.52 | GCA_036453235.1 | S2 |
LCO2 | Bacillota A | CAG-791 sp900315055 | GCA_900315055.1 | 0.9889 | MQ | 94.91 | 0.4 | 2,906,087 | 106 | 37,633 | 55.88 | GCA_036453225.1 | A2 |
LCO3 | Bacillota A | Bilifractor | N/A | N/A | MQ | 91.56 | 1.27 | 2,395,184 | 17 | 174,318 | 50.59 | GCA_036453165.1 | S1 |
LCO4 | Bacillota A | UBA1066 | N/A | N/A | MQ | 89.81 | 0 | 2,176,431 | 67 | 54,455 | 55.06 | GCA_036453195.1 | A2 |
ACUT1 | Bacillota A | Caproicibacterium sp022483045 | GCA_022483045.1 | 0.9999 | MQ | 82.55 | 0 | 1,598,564 | 22 | 86,104 | 51.34 | GCA_036454745.1 | A3 |
ACUT2 | Bacillota A | Caproicibacterium sp902809935 | GCA_902809935.1 | 0.9948 | MQ | 82.7 | 0.34 | 1,580,463 | 82 | 22,595 | 42.65 | GCA_036454725.1 | S2 |
ENTER1 | Pseudomonadota | Rahnella inusitata | GCF_003263515.1 | 0.9896 | MQ | 98.03 | 0.08 | 5,063,486 | 10 | 2,624,760 | 53.06 | GCA_036453825.1 | S2 |
ACET1 | Pseudomonadota | Acetobacter sp012517935 | GCA_012517935.1 | 0.958 | MQ | 100 | 0.25 | 2,793,541 | 28 | 121,035 | 53.7 | GCA_036452275.1 | A2 |
PSEU1 | Pseudomonadota | Pseudomonas E helleri | GCF_001043025.1 | 0.9728 | MQ | 75.79 | 0 | 5,159,292 | 131 | 53,203 | 58.58 | GCA_036452715.1 | S2 |
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Walters, K.A.; Myers, K.S.; Ingle, A.T.; Donohue, T.J.; Noguera, D.R. Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture. Fermentation 2024, 10, 422. https://doi.org/10.3390/fermentation10080422
Walters KA, Myers KS, Ingle AT, Donohue TJ, Noguera DR. Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture. Fermentation. 2024; 10(8):422. https://doi.org/10.3390/fermentation10080422
Chicago/Turabian StyleWalters, Kevin A., Kevin S. Myers, Abel T. Ingle, Timothy J. Donohue, and Daniel R. Noguera. 2024. "Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture" Fermentation 10, no. 8: 422. https://doi.org/10.3390/fermentation10080422