Table 2.
The main factors affect the microbial colonization of young calves
| Factors | Age and breed | Treatment | Conclusions |
|---|---|---|---|
| Colostrum | Holstein calves at 6 h and 12 h after birth | Calves were in three groups: fresh colostrum (FC, n = 12); heat-treated colostrum (HC, 60 °C for 60 min, n = 12); no colostrum (NC, n = 8) | Fresh and heat-treated colostrum feeding increased Bifidobacterium and inhibited E. coli colonization in the colon of newborn calves [38] |
| Holstein calves at 6 h and 12 h after birth | Calves were in three groups: fresh colostrum (FC, n = 12); heat-treated colostrum (HC, 60 °C for 60 min, n = 12); no colostrum (NC, n = 8) | Heat-treated colostrum feeding enhanced tissue-attached Bifidobacterium colonization while reducing E. coli colonization in the small intestine of calves [7] | |
| Holstein calves at 51 h after birth | Calves (n = 27) were randomly assigned to three groups: fed colostrum at 45 min (0 h, n = 9), 6 h (n = 9), or 12 h (n = 9) after birth | Delayed colostrum feeding by 6 or 12 h reduced IgG absorption efficiency and delayed mucosa-attached Bifidobacterium spp., Lactobacillus spp., and E. coli colonization [6] | |
| Holstein calves at 51 h after birth | Calves (n = 27) were randomly assigned to three groups: fed colostrum at 45 min (0 h, n = 9), 6 h (n = 9), or 12 h (n = 9) after birth | Delaying first colostrum feeding to 12 h after birth significantly increased the relative abundance of ileum mucosa-associated Enterococcus and Streptococcus, while reducing colon mucosa-associated Lactobacillus [39] | |
| Milk replacer/whole milk | Holstein–Friesian dairy calves at 0, 7, 14, 28, and 49 d after first consumption of milk replacer | Calves (n = 10) were assigned to two groups fed different milk replacers: MR1 (n = 5, 55% crude protein from whey, higher free milk oligosaccharides) or MR2 (n = 5, 74% crude protein from whey protein phospholipid concentrate, higher conjugated milk oligosaccharides) | Calves fed MR2 showed significantly greater relative abundance of Bifidobacterium spp. and Faecalibacterium prausnitzii at d 7 compared to MR1-fed calves [42] |
| Kiwi cross calves (Holstein–Friesian x Jersey) at pre-weaning (67 ± 3 d on trial) | Calves (n = 199) were assigned to three milk replacer allowance groups using automated feeders: low allowance (LA, 10% of initial body weight/d, n = 67), high allowance (HA, 20% of initial body weight/d, n = 65), or ad libitum (ADLIB, n = 66) | Higher milk replacer allowances increased hindgut bacterial diversity, and abundances of beneficial Faecalibacterium spp. [43] | |
| Holstein female calves from birth to 98 d of age | Calves (n = 48) were randomly assigned to two groups: high milk (HM, n = 24, 20% of birth BW for the first 3 weeks, then gradually reduced to 10% until weaning on d 51) or low milk (LM, n = 24, 10% of birth BW throughout). Fecal samples were collected on d 7, 14, and 21 | Higher milk allowance improved fecal Lactobacillus, and inhibited Escherichia coli. Higher milk allowance calves exhibited lower serum TNF-α and cortisol levels on d 14 and 28, fewer days with fever and greater body weight at d 21, 56, and 98 [44] | |
| Calf starter | Male yak calves (Bos grunniens) from 30 to 120 d of age | Calves (n = 20) were randomly assigned to four groups: milk replacer only (CON, n = 5), milk replacer + alfalfa hay (A, n = 5), milk replacer + starter feed (S, n = 5), or milk replacer + starter feed + alfalfa hay (SA, n = 5) | Co-supplementation with alfalfa hay and starter feed (SA group) significantly improved growth performance and increased caecal VFA concentrations while maintaining immune homeostasis. While starter feed alone (S group) significantly increased caecal lactate and LPS contents, leading to elevated plasma cortisol, NO, TNF-α, and IFN-γ levels indicative of inflammation [8] |
| Holstein bull calves at 49 ± 5.2 d of age | Calves (n = 8) were paired by BW and assigned to two groups: milk replacer only (MR, 750 g/d, n = 4) or milk replacer + calf starter (MR + S, starter ad libitum, n = 4) | Calf starter feeding tended to increase bacterial phylotype richness along the GIT and significantly altered mucosal immune gene expression [45] | |
| Roughage | Holstein calves from 3 d to weaning (50 d) | Calves (n = 20) were divided into control (n = 10) or treatment (n = 10) groups. Treatment calves received oral administration of ground timothy hay and psyllium (50:6 ratio) at 50 g/d from 3–7 d and 100 g/d from 8 d until weaning. Fecal samples were collected at 7, 21, 35, 49, and 56 d | Oral fiber administration improved ADG during the first 21 days of life and increased fecal propionate proportion at 7 d. Lactobacillus and Prevotellaceae were enriched at 7 d, while C. perfringens detection was reduced [52] |
| Holstein dairy cows from 2 weeks to first lactation cycle (~ 2 years) | Holstein calves (n = 45) were assigned to three groups: calf starter grains, corn silage, or a 25:75 starter/silage mixture | Significant diet-associated differences in fecal archaeal and bacterial communities were observed by weaning (8 weeks), with silage-fed calves achieving a more adult-like microbiota composition earlier than starter-fed calves [53] | |
| Prebiotics/Probiotics/Synbiotics | Holstein calves from 1–4 d to 8 weeks of age | Calves (n = 80) were randomly assigned to two groups: control milk replacer (CON, n = 40) or GOS-supplemented milk replacer (GOS, n = 40). At 2 and 4 weeks, 8 calves per treatment were euthanized for intestinal digesta and tissue collection. The remaining 48 calves continued to week 8 | GOS supplementation significantly increased colonic Lactobacillus and Bifidobacterium relative abundance at 2 weeks of age, while reducing Fecalibacterium, Oscillospira, and Clostridium. Additionally, GOS-fed calves showed greater intestinal villus length in duodenum, jejunum, and deeper colonic crypts, but also exhibited lower colonic digesta DM [9] |
| Crossbred calves (Japanese Black × Holstein) from approximately 11–20 d of age to weaning (~ 72 d) | Experiment 1: Calves (n = 173) were divided into control (n = 83) and trehalose (n = 90) groups. Experiment 2: Male calves (n = 20) were divided into control (n = 10) and trehalose (n = 10) groups | Trehalose significantly reduced medication frequency, reduced Clostridium spp. and enriched fiber-degrading bacteria Prevotella and Lachnospira by weaning [57] | |
| Chinese Holstein female calves from 6 ± 3 d to 8 weeks of age | Calves (n = 40) were assigned to four groups: control (C, n = 10), T1 (0.5 g MSP/calf/d, n = 10), T2 (1 g MSP/calf/d, n = 10), or T3 (2 g MSP/calf/d, n = 10). MSP contained Lactobacillus acidophilus (3 × 109 CFU/g), Bacillus subtilis (3 × 109 CFU/g), and Saccharomyces cerevisiae (1 × 109 CFU/g). Fecal samples were collected at week 2, week 4, week 6 and week 8 | High-dose MSP (2 g/d, T3) increased Bifidobacterium, Lactobacillus, and Collinsella abundances and reduced diarrhea incidence in pre-weaning calves at week 2 [60] | |
| Holstein calves from 5–9 d to 21 d | Calves (n = 30) were assigned to three groups: control (n = 10), Limosilactobacillus reuteri TP1.3B (n = 10), or Lactobacillus johnsonii TP1.6 (n = 10) | High relative abundance of Bifidobacterium and Akkermansia were displayed in both treated groups compared to control [61] | |
| Murrah buffalo calves from 5–7 d to 60 d of age | Calves (n = 16) were in four treatments: control (CT, n = 4), Limosilactobacillus reuteri BF-E7 (LR, 1 × 108 CFU/g/d, n = 4), Ligilactobacillus salivarius BF-17 (LS, 1 × 108 CFU/g/d, n = 4), or consortium of both strains (CS, 1 × 108 CFU/g/d, n = 4) | Probiotics supplementation increased dry matter intake (DMI, g/d), average daily gain, net body weight gain, feed conversion efficiency, and structural growth measurements, as well as the relative abundance of Lactobacillus and Bifidobacteria compared to control [62] | |
| Japanese Black calves from 2–12 d to 3 weeks after separation | Calves (n = 10) were in two treatments: control (n = 5) or HK-LS HS-1 supplement (n = 5) | HK-LS HS-1 supplementation significantly increased fecal lactic acid bacteria counts on d 21 and reduced medication frequency and treatment costs compared to control [63] | |
| Newborn Simmental calves from 2 to 14 d of age | Calves (n = 166) from 10 dairy farms were assigned to two groups: control and L. reuteri group | L. reuteri administration significantly reduced diarrhea incidence within the first 2 weeks of life, with the protective effect most pronounced between d 3 and 10 [64] | |
| Male Holstein calves from birth to 1 week of age | Calves (n = 20) were randomly assigned to two groups: control (CON, n = 10) or SCB (n = 10, 5 g/d live S. cerevisiae boulardii CNCM I-1079, 10 × 109 CFU/d). At 1 week, calves were euthanized and digesta/tissue samples from proximal jejunum, ileum, and colon were collected | SCB supplementation significantly increased species richness and phylogenetic diversity in ileum digesta. SCB enriched Eubacteriaceae, Corynebacteriaceae, Eggerthellaceae, Bacillaceae, and Ruminococcaceae families [65] | |
| Dairy calves from 2–7 d to 96 d of age | Calves (n = 32) were randomly assigned to four groups: control (CTL, n = 8), S. cerevisiae boulardii CNCM I-1079 (SCB, 7.5 × 108 CFU/L milk replacer + 3 × 109 CFU/kg starter, n = 8), L. acidophilus BT1386 (LA, 2.5 × 108 CFU/L milk replacer + 1 × 109 CFU/kg starter, n = 8), or antibiotic growth promoter (ATB, chlortetracycline + neomycin, n = 8). Digesta from rumen, ileum, and colon, and mucosa from ileum and colon were collected at d 33 (pre-weaning) and d 96 | Both SCB and LA reduced pathogenic Streptococcus and Tyzzerella_4 and increased beneficial Fibrobacter, with effects predominantly in the ileum during pre-weaning. SCB specifically enriched Roseburia and Olsenella. SCB and LA had similar impact on diversity as ATB but more diverse effects on bacterial composition [66] | |
| Murrah buffalo calves from 5 to 80 d of age | Calves (n = 24) were divided into four groups: control (CON, n = 6), SYN1 (3 g FOS + L. plantarum CRD-7 in 150 mL fermented milk, n = 6), SYN2 (6 g FOS + L. plantarum CRD-7 in 100 mL fermented milk, n = 6), or SYN3 (9 g FOS + L. plantarum CRD-7 in 50 mL fermented milk, n = 6). Synbiotics were administered daily for 75 d | Calves in SYN3 displayed improved digestibility, antioxidant enzymes, and immune status, along with increased Lactobacilli and Bifidobacterium counts and reduced diarrhea incidence [67] | |
| Crossbred (Sahiwal × Holstein Friesian) calves from 15 to 105 d of age | Calves (n = 24) were divided into four groups: control (T0, n = 6), probiotic (T1, n = 6, L. acidophilus 2 × 1010 CFU/g @ 1 g/calf/d), prebiotic (T2, n = 6, MOS 4 g/calf/d), or synbiotic (T3, n = 6, L. acidophilus 0.5 g + MOS 2 g/calf/d). Additives were mixed in milk and fed for 90 d | Probiotic and synbiotic groups showed significantly higher total body weight gain and DM digestibility. All treatment groups reduced fecal coliform and E. coli counts at d 15 and 30 [68] | |
| Murrah buffalo calves from 5–7 d to 120 d of age | Calves (n = 20) were divided into four groups: control (CON, n = 5), prebiotic (PRE, n = 5, MOS 4 g/calf/d), probiotic (PRO, n = 5, L. acidophilus fermented milk 200 mL/d containing 108 CFU/mL), or synbiotic (SYN, n = 5, MOS + L. acidophilus at same doses). Fecal samples were collected at d 0, 30, 60, 90, and 120 | Synbiotic supplementation significantly improved ADG and NDF digestibility compared to control. All treatments increased fecal Lactobacillus and Bifidobacterium while reducing coliform counts. Fecal pH and ammonia decreased, while VFA (acetate, propionate, butyrate) increased. Synbiotic showed greatest effects, suggesting MOS and L. acidophilus combination optimally improves performance and gut health [69] | |
| Holstein heifer calves from 4–12 h of age to weaning at 60 d | Calves (n = 1801) were in four groups: control (CON, n = 450), prebiotic (PRE, 14 mL yeast culture enriched with MOS, n = 450), probiotic (PRO, 1 g Bacillus subtilis + Lactobacillus plantarum, 1 × 109 + 2.5 × 108 CFU/d, n = 451), or synbiotic (SYN, combination of PRE and PRO, n = 450) | Synbiotic supplementation increased overall ADG by 19 g/d compared to control. During late preweaning (42–56 d), PRE and SYN increased ADG by 85 and 78 g/d, respectively. Probiotic reduced Cryptosporidium shedding 100-fold at 14 d. Prebiotic reduced fecal E. coli and pathogenic E. coli at 42 d [70] | |
| Antibiotics | Male Holstein calves from birth to 6 weeks of age | Calves (n = 30) were randomly assigned to two groups: no drug residues (NR, n = 15, raw milk without antimicrobials) or drug residues (DR, n = 15, raw milk spiked with ceftiofur 0.1 μg/mL, penicillin G 0.005 μg/mL, ampicillin 0.01 μg/mL, and oxytetracycline 0.3 μg/mL). Fecal samples were collected weekly from birth (pre-treatment) to 6 weeks | Discriminant analysis showed clear separation between DR and NR calves at the genus level from week 1 onwards, indicating that drug residues at FDA tolerance levels affect gut microbiota composition. Additionally, Clostridium (P = 0.03) and Streptococcus (P = 0.004) were significantly reduced in DR calves [11] |
| Male Holstein calves from birth to 6 weeks of age | Calves (n = 14) were assigned to two groups: control (NR, n = 7, raw milk without antimicrobials) or drug residues (DR, n = 7, raw milk spiked with ceftiofur 0.1 μg/mL, penicillin G 0.005 μg/mL, ampicillin 0.01 μg/mL, and oxytetracycline 0.3 μg/mL). Calves were bucket-fed one gallon of milk twice daily. Fecal samples were collected at weeks 0, 1, 3, and 6 | Drug residues significantly altered fecal microbiota functional profiles, with decreased "Stress Response", "Regulation and Cell Signaling", and "Nitrogen Metabolism" genes in DR calves at week 1. Drug residues also resulted in more homogeneous RATC profiles over time, suggesting selective pressure on resistance gene distribution [74] | |
| Holstein calves from 1 to 35 d of age | Calves (n = 12) were assigned to three groups: control (CON, n = 4, milk replacer without antibiotics), low cocktail of antibiotics (LCA, n = 4, penicillin 0.024 mg/L + streptomycin 0.025 mg/L + tetracycline 0.1 mg/L + ceftiofur 0.33 mg/L), or low single antibiotic (LSA, n = 4, ceftiofur 0.33 mg/L only). Antibiotics were added to MR and fed twice daily. At 35 d, calves were euthanized and digesta from ileum, colon, and rectum were collected | LCA significantly reduced ileal Enterobacteriaceae and Escherichia coli, while LSA reduced Comamonas. In the rectum, both LCA and LSA reduced Acidaminococcaceae and Phascolarctobacterium [75] | |
| Japanese Black calves from 3 to 60 d of age | Calves (n = 12) were assigned to CON (n = 6, milk replacer containing CTC at 10 g/kg) or EXP (n = 6, antibiotic-free milk replacer). Fecal samples were collected at 3, 30, and 60 d | CTC altered weighted UniFrac distances at 60 d and increased methanogens Methanobrevibacter, while antibiotic-free calves showed higher Lachnospiraceae [76] | |
| Fecal transplantation | Korean brown cattle (Bos taurus coreanae) calves aged 5–50 d with moderate-to-severe diarrhea | Diarrheic calves (n = 57) were assigned to three groups: control (CON, n = 14, saline), antibiotic (ABX, n = 23, neomycin ± other antibiotics), or FMT (n = 20, 5 g feces as bolus at 0.1 g/mL, administered orally 5 times). Healthy donor calves (n = 6, aged 21–50 d) were rigorously screened. Fecal samples were collected at d 0, 2, 4, 8, 16, 32, and 48 | FMT achieved 95% complete remission rate vs. 35.7% (CON) and 26.1% (ABX), with 0% mortality vs. 14.3% and 17.4%. FMT increased Porphyromonadaceae abundance, which negatively correlated with diarrhea (r = −0.714, P = 0.041), while reducing Enterobacteriaceae [12] |
| Chinese Holstein calves from 50 d (weaning) to 80 d of age | Calves (n = 50) were divided into five groups: NC (n = 10, no supplementation), Control (n = 10, 5 mL saline), LFMT (n = 10, 5 mL of 1 × 108 CFU/mL fecal suspension), HFMT (n = 10, 5 mL of 1 × 109 CFU/mL), or SFMT (n = 10, sterilized fecal suspension). Treatments were administered orally every other day from d 50 to 60. Fecal samples were collected at d 5, 10, 15, and 20 post-weaning | FMT significantly enhanced the relative abundance of beneficial bacteria, such as Blautia, Lactobacillus, Ruminococcus and Romboutsia. Diarrhea rates were significantly reduced, with the LFMT group showing the most pronounced effect [47] | |
| Holstein, Jersey, and Jersey-cross heifer calves from 4–12 d to 21 d of age | Calves (n = 227) were assigned to control (n = 115, standard farm protocol) or FMT (n = 112, ~ 36 g processed fecal matter orally once daily for 3 d) | Calves were less likely to recover from diarrhea and more likely to die after FMT. Higher relative abundance of Lactobacillus and Lactobacillus reuteri and lower relative abundance of Clostridium nexile and Bacteroides vulgatus on d 10 were detected [77] | |
| Health and diarrheic calves, and the trail lasted for 7 d after FMT | Twenty FMT treatments were conducted: healthy donors (n = 20) and diarrheal recipients (n = 20) were selected from the same farm | Sporobacter genus and metabolites such as glycerol 3-phosphate, dihydroxyacetone phosphate, and isoamylamine could serve as biomarkers for donor selection [78] | |
| Transportation | Limousine beef steers, approximately of 6–10 months | Nasopharyngeal swabs were collected from 231 calves at three time points: before transportation from the origin farm, within four days of arrival at the feedlot, and during clinical examination of each calf at the feedlot | Bovine coronavirus (BCoV, 70.1%) and Histophilus somni (86.6%) were the most prevalent viral and bacterial pathogens in nasopharyngeal swabs of transported cattle, with a significant association observed between Mannheimia haemolytica positivity and respiratory clinical signs. The nasopharyngeal microbiota was significantly affected by long-distance transportation, suggesting that enhancing calf immunity prior to loading may be more effective in reducing BRD risk [79] |
| Surplus dairy calves at 1–19 days old from 5 commercial dairy farms in Ontario, Canada | Calves (n = 177) were randomly assigned to three transport duration groups: 6 h (T1, n = 59), 12 h (T2, n = 60), and 16 h (T3, n = 58). Fecal samples were collected at four time points: before transport (0 h), immediately after transport (AT), 24 h post-transport, and 72 h post-transport | Longer transport duration (16 h) significantly reduced Fusobacteria abundance compared to 6 h. Lactobacillus decreased while Bacteroides and Butyricicoccus increased over time, with Firmicutes declining within 72 h post-transport [80] | |
| Simmental calves, approximately 0.5 years old | Nasopharyngeal swabs were collected from calves (n = 112) at three key time points: 6 h prior to loading (Group A), immediately after unloading (Group B), and after 7-day placement (Group C) | Prior to transportation, the nasopharyngeal microbiota of calves was dominated by potential bovine respiratory disease (BRD)-related pathogens, such as Moraxella, Mannheimia, and Acinetobacter. After 7 days of adaptive placement, there is a noticeable decrease in the abundance of these pathogens [81] | |
| Simmental crossbred calves (~ 8 months old) subjected to 30 h road transportation | Calves (n = 60) were transported 30 h from Jilin Province to Sichuan Province, China. The AMW group (n = 30) received AMW supplementation (30 mL/calf/d) for 3 d before and 30 d after transportation, while the Control group (n = 29) received no supplementation. Nasopharyngeal swabs were collected on d −3, 30, and 60 | AMW-supplemented calves showed significantly lower rectal temperatures, respiratory scores, and nasal discharge scores, with higher body weight gain. compared to controls. AMW supplementation altered nasopharyngeal microbiota composition and enhanced peripheral immunity, intestinal absorption, and lipogenesis [82] | |
| Heat stress | Male Holstein calves from birth to 68 days of age | Calves (n = 60) were divided into three groups: control (n = 20, wire hutches outdoors with 50% plywood cover), SH (n = 21, wire hutches in open-sided barn without fans), or SHF (n = 19, wire hutches in open-sided barn with ceiling fans). Nasal swabs were collected at week 5 and week 9 | On week 5, the SHF group showed significantly lower mean relative abundance of Mycoplasma compared to the control and SH groups, on week 9, Control calves exhibited a lower mean relative abundance of Escherichia compared to the SHF calves, while showing a higher mean relative abundance of Moraxella than those in the SH and SHF groups [83] |
| Holstein calves at 1–28 days of life | Calves (n = 16) were divided into four groups: Control (n = 4); low SB (LSB, n = 4), control milk replacer supplemented with 0.5 g of SB (n = 4); medium SB (MSB, n = 4), control milk replacer supplemented with 1.0 g of SB n = 4; high SB (HSB, n = 4), control milk replacer supplemented with 2.0 g of SB | SB supplementation decreased the fecal densities of E. coli and Enterobacteriaceae during the thermal neutral (TN) period, but no significant effects were observed during the heat stress (HS) period [85] | |
| Pre-weaning Holstein calves during summer | Calves (n = 20) were divided into two groups based on their response to heat stress: a high HS response group (H, n = 10) and low HS response group (L, n = 10) | Calves in H group had higher rectal temperatures and respiratory rates, as well as higher serum concentrations of IL-2, HSP-70, and total fatty acids (TFA) and etc., lower abundance of ruminal Ruminococcus and Olsenella, and downregulated pathways related to pyruvate metabolism and the TCA cycle [86] |