Repeated Inoculation of Young Calves With Rumen Microbiota Does Not Significantly Modulate the Rumen Prokaryotic Microbiota Consistently but Decreases Diarrhea

Influence of empirically derived filtering parameters, amplicon sequence variant, and operational taxonomic unit pipelines on assessing rumen microbial diversity

Microbes play an important role in human and animal health, as well as animal productivity. The host microbial interactions within ruminants play a critical role in animal health and productivity and provide up to 70% of the animal's energy needs in the form of fermentation products. As such, many studies have investigated microbial community composition to understand the microbial community changes and factors that affect microbial colonization and persistence. Advances in next-generation sequencing technologies and the low cost of sequencing have led many studies to use 16S rDNA-based analysis tools for interrogation of microbiomes at a much finer scale than traditional culturing. However, methods that rely on single base pair differences for bacterial taxa clustering may inflate or underestimate diversity, leading to inaccurate identification of bacterial diversity. Therefore, in this study, we sequenced mock communities of known membership and abundance to establish filtration parameters to reduce the inflation of microbial diversity due to PCR and sequencing errors. Additionally, we evaluated the effect of the resulting filtering parameters proposed using established bioinformatic pipelines on a study consisting of Holstein and Jersey cattle to identify breed and treatment effects on the bacterial community composition and the impact of filtering on global microbial community structure analysis and results. Filtration resulted in a sharp reduction in bacterial taxa identified, yet retain most sequencing data (retaining >79% of sequencing reads) when analyzed using 3 different microbial analysis pipelines (DADA2, Mothur, USEARCH). After filtration, conclusions from α-diversity and β-diversity tests showed very similar results across all analysis methods. The mock community-based filtering parameters proposed in this study help provide a more realistic estimation of bacterial diversity. Additionally, filtration reduced the variation between microbiome analysis methods and helped to identify microbial community differences that could have been missed due to the large animal-to-animal variation observed in the unfiltered data. As such, we believe the new filtering parameters described in this study will help to obtain diversity estimates that are closer to realistic values, improve the ability to detecting microbial community differences, and help to better understand microbial community changes in 16S rDNA-based studies.

Fecal microbiota colonization dynamics in dairy heifers associated with early-life rumen microbiota modulation and gut health

Early-life modulation of rumen microbiota holds promise for enhancing calf growth, health, and long-term production in ruminants. However, limited attention has been given to the impact of rumen microbiota modulation on the establishment of hindgut microbiota. In this study, fecal microbiota development was examined in identical twin calves for 12 months. The treatment group (T-group) received adult cow fresh rumen liquid inoculum during the pre-weaning period, while the control group did not (C-group). The effects of inoculum were assessed on calf gut health and as microbial seeding route into the hindgut. The early rumen modulation had no effect on age-related fecal microbiota development. The fecal bacterial community evolved gradually following dietary changes and categorized into pre-weaning and post-weaning communities. Bacterial richness increased with age and stabilized at month 9, while between-sample variation reduced in post-weaning samples. Archaeal load in fecal samples increased after month 4, while archaeal richness increased and stabilized in both groups by month 9. Between-sample similarity was higher during the pre-weaning period, with increased dissimilarity from month 4 onward. Anaerobic fungi were detected in feces at month 4, with richness peaking at month 7. Before month 6, fungal community composition distinctly differed from mature communities. When colostrum, calf rumen, and donor inoculum were evaluated as seeding sources for hindgut colonization, the calf's own rumen was identified as the primary seeding source for fecal bacteria and fungi. Colostrum was a source for several bacteria detected in feces, but these were of temporary importance until weaning. The donor inoculum had limited impact on gut health as diarrhea rates were similar between the T-group and C-group. In conclusion, early-life microbiota modulation shows potential in ruminant development. However, a more targeted approach with bacteria adapted to the hindgut environment may be necessary to modulate hindgut effectively. This research contributes to our understanding of the complex relationship between gut microbiota and calf health and growth.

- Invited Review - Ruminal ciliates as modulators of the rumen microbiome

Ruminal ciliates are a fundamental constituent within the rumen microbiome of ruminant animals. The complex interactions between ruminal ciliates and other microbial guilds within the rumen ecosystems are of paramount importance for facilitating the digestion and fermentation processes of ingested feed components. This review underscores the significance of ruminal ciliates by exploring their impact on key factors, such as methane production, nitrogen utilization efficiency, feed efficiency, and other animal performance measurements. Various methods are employed in the study of ruminal ciliates including culture techniques and molecular approaches. This review highlights the pressing need for further investigations to discern the distinct roles of various ciliate species, particularly relating to methane mitigation and the enhancement of nitrogen utilization efficiency. The promotion of establishing robust reference databases tailored specifically to ruminal ciliates is encouraged, alongside the utilization of genomics and transcriptomics that can highlight their functional contributions to the rumen microbiome. Collectively, the progressive advancement in knowledge concerning ruminal ciliates and their inherent biological significance will be helpful in the pursuit of optimizing rumen functionality and refining animal production outcomes.

Growth Performance and Fecal Microbiota of Dairy Calves Supplemented with Autochthonous Lactic Acid Bacteria as Probiotics in Mexican Western Family Dairy Farming

Probiotic supplementation in dairy cattle has achieved several beneficial effects (improved growth rate, immune response, and adequate ruminal microbiota). This study assessed the effects on the growth parameters and gut microbiota of newborn dairy calves supplemented with two Lactobacillus-based probiotics, individually (6BZ or 6BY) or their combination (6BZ + 6BY), administrated with the same concentration (1 × 109 CFU/kg weight) at three times, between days 5 and 19 after birth. The control group consisted of probiotic-unsupplemented calves. Growth parameters were recorded weekly until eight weeks and at the calves' ages of three, four, and five months. Fecal microbiota was described by high-throughput sequencing and bioinformatics. Although no significant effects were observed regarding daily weight and height gain among probiotic-supplemented and non-supplemented calves, correlation analysis showed that growth rate was maintained until month 5 through probiotic supplementation, mainly when the two-strain probiotics were supplied. Modulation effects on microbiota were observed in probiotic-supplemented calves, improving the Bacteroidota: Firmicutes and the Proteobacteria ratios. Functional prediction by PICRUSt also showed an increment in several pathways when the two-strain probiotic was supplemented. Therefore, using the three-administration scheme, the two-strain probiotic improved the growth rate and gut microbiota profile in newborn dairy calves. However, positive effects could be reached by applying more administrations of the probiotic during the first 20 days of a calf's life.

Ruminal Fluid Transplantation Accelerates Rumen Microbial Remodeling and Improves Feed Efficiency in Yaks

A relatively stable microbial ecological balance system in the rumen plays an important role in rumen environment stability and ruminant health maintenance. No studies have reported how rumen fluid transplantation (RFT) affects the composition of rumen microorganisms and yak growth performance. In this experiment, we transplanted fresh rumen fluid adapted to house-feeding yaks to yaks transitioned from natural pastures to house-feeding periods to investigate the effects of rumen fluid transplantation on rumen microbial community regulation and production performance. Twenty yaks were randomly divided into the control group (CON; n = 10) and the rumen fluid transplantation group (RT; n = 10). Ten yaks that had been adapted to stall fattening feed in one month were selected as the rumen fluid donor group to provide fresh rumen fluid. Ruminal fluid transplantation trials were conducted on the 1st, 3rd, and 5th. Overall, 1 L of ruminal fluid was transplanted to each yak in the RT and CON group. The formal trial then began with both groups fed the same diet. After this, growth performance was measured, rumen fluid was collected, and rumen microbial composition was compared using 16s rRNA sequencing data. The results showed that rumen fluid transplantation had no significant effect on yak total weight gain or daily weight gain (p > 0.05), and feed efficiency was higher in the RT group than in the CON group at 3 months (treatment × month: p < 0.01). Ruminal fluid transplantation significantly affected rumen alpha diversity (p < 0.05). Up to day 60, the RT group had significantly higher OTU numbers, Shannon diversity, and Simpson homogeneity than the CON group. Principal coordinate analysis showed that the rumen microbiota differed significantly on days 4 and 7 (p < 0.05). Bacteroidota, Firmicutes, Proteobacteria, and Spirochaetes were the most abundant phyla in the rumen. The relative abundances of Bacteroidota, Proteobacteria, and Spirochaetes were lower in the RT group than in the CON group, with a decrease observed in Bacteroidota in the RT group on days 7 and 28 after rumen fluid transplantation (p = 0.013), while Proteobacteria showed a decreasing trend in the CON group and an increasing trend in RT; however, this was only at day 4 (p = 0.019). The relative abundance of Firmicutes was significantly higher in the RT group than in the CON group on days 4, 7, and 28 (p = 0.001). Prevotella and Rikenellaceae_RC9_gut_group were the predominant genera. In conclusion, our findings suggest that rumen fluid transplantation improves yak growth performance and rumen microbial reshaping. The findings of this study provide new insights into yak microbial community transplantation and a reference for improving feed efficiency in the yak industry.

Modulating gastrointestinal microbiota to alleviate diarrhea in calves

The calf stage is a critical period for the development of heifers. Newborn calves have low gastrointestinal barrier function and immunity before weaning, making them highly susceptible to infection by various intestinal pathogens. Diarrhea in calves poses a significant threat to the health of young ruminants and may cause serious economic losses to livestock farms. Antibiotics are commonly used to treat diarrhea and promote calf growth, leading to bacterial resistance and increasing antibiotic residues in meat. Therefore, finding new technologies to improve the diarrhea of newborn calves is a challenge for livestock production and public health. The operation of the gut microbiota in the early stages after birth is crucial for optimizing immune function and body growth. Microbiota colonization of newborn animals is crucial for healthy development. Early intervention of the calf gastrointestinal microbiota, such as oral probiotics, fecal microbiota transplantation and rumen microbiota transplantation can effectively relieve calf diarrhea. This review focuses on the role and mechanisms of oral probiotics such as Lactobacillus, Bifidobacterium and Faecalibacterium in relieving calf diarrhea. The aim is to develop appropriate antibiotic alternatives to improve calf health in a sustainable and responsible manner, while addressing public health issues related to the use of antibiotics in livestock.

Sodium butyrate supplementation impacts the gastrointestinal bacteria of dairy calves before weaning

The objective of this study was to systematically investigate how sodium butyrate (SB) affects the gastrointestinal bacteria in newborn calves at different stages before weaning. Forty female newborn Holstein calves (4-day-old, 40 ± 5 kg of body weight) were randomly divided into four groups; each group was supplemented with four SB doses: 0, 15, 30, and 45 g/day (ten replicates) in SB0, SB15, SB30, and SB45 groups, respectively. SB was fed with milk replacer from day 4 to day 60. Rumen fluid and feces were collected on days 2, 14, 28, 42, and 60 for 16S rRNA high-throughput sequencing. Data were analyzed in a complete randomized design and analyzed on the online platform of Majorbio Cloud Platform. The results showed that SB significantly increased the α-diversity in feces, especially Shannon and Chao indices in SB45 and SB30 at day 60 more than in SB15 (P < 0.05). Additionally, SB significantly enhanced Firmicutes growth from day 2 to 28 and also increased Bacteroides abundance from day 28 to 42 in rumen and feces (P < 0.05). SB also significantly inhibited Proteobacteria abundance in rumen and feces during the study period (P < 0.05). SB also promoted some potential beneficial bacterial abundance, including Prevotella, Lachnospiraceae, Clostridium, Ruminococcus, and Muribaculaceae (P < 0.05). Additionally, Escherichia-Shigella abundance at SB0 was significantly lower than in the other groups (P < 0.05). In conclusion, this study firstly reported a dynamic curve showing of the SB effects on bacteria in calves before weaning. This study provides valuable evidence for the development of the gastrointestinal tract of the calves in the early stage of the life. SB supplementation improved the gastrointestinal health by regulating the bacterial populations. KEY POINTS: • The gastrointestinal tract of calves has been improved after the SB supplementation. • Microbes were the vital influential factor in the development of calves. • Intervention before weaning is an effective strategy for calf health.

Dynamic distribution of gut microbiota in cattle at different breeds and health states

Weining cattle is a precious species with high tolerance to cold, disease, and stress, and accounts for a large proportion of agricultural economic output in Guizhou, China. However, there are gaps in information about the intestinal flora of Weining cattle. In this study, high-throughput sequencing were employed to analyze the intestinal flora of Weining cattle (WN), Angus cattle (An), and diarrheal Angus cattle (DA), and explore the potential bacteria associated with diarrhea. We collected 18 fecal samples from Weining, Guizhou, including Weining cattle, Healthy Angus, and Diarrheal Angus. The results of intestinal microbiota analysis showed there were no significant differences in intestinal flora diversity and richness among groups (p > 0.05). The abundance of beneficial bacteria (Lachnospiraceae, Rikenellaceae, Coprostanoligenes, and Cyanobacteria) in Weining cattle were significantly higher than in Angus cattle (p < 0.05). The potential pathogens including Anaerosporobacter and Campylobacteria were enriched in the DA group. Furthermore, the abundance of Lachnospiraceae was very high in the WN group (p < 0.05), which might explain why Weining cattle are less prone to diarrhea. This is the first report on the intestinal flora of Weining cattle, furthering understanding of the relationship between intestinal flora and health.

Dynamic changes of gut fungal community in horse at different health states

Accumulating studies indicated that gut microbial changes played key roles in the progression of multiple diseases, which seriously threaten the host health. Gut microbial dysbiosis is closely associated with the development of diarrhea, but gut microbial composition and variability in diarrheic horses have not been well characterized. Here, we investigated gut fungal compositions and changes in healthy and diarrheic horses using amplicon sequencing. Results indicated that the alpha and beta diversities of gut fungal community in diarrheal horses changed significantly, accompanied by distinct changes in taxonomic compositions. The types of main fungal phyla (Neocallimastigomycota, Ascomycota, and Basidiomycota) in healthy and diarrheal horses were same but different in relative abundances. However, the species and abundances of dominant fungal genera in diarrheal horses changed significantly compared with healthy horses. Results of Metastats analysis indicated that all differential fungal phyla (Blastocladiomycota, Kickxellomycota, Rozellomycota, Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Neocallimastigomycota, Glomeromycota, and Olpidiomycota) showed a decreasing trend during diarrhea. Moreover, a total of 175 differential fungal genera were identified for the gut fungal community between healthy and diarrheal horses, where 4 fungal genera increased significantly, 171 bacterial genera decreased dramatically during diarrhea. Among these decreased bacteria, 74 fungal genera even completely disappeared from the intestine. Moreover, this is the first comparative analysis of equine gut fungal community in different health states, which is beneficial to understand the important role of gut fungal community in equine health.

Alterations in gut microbiota and metabolites associated with altitude-induced cardiac hypertrophy in rats during hypobaric hypoxia challenge

The gut microbiota is involved in host responses to high altitude. However, the dynamics of intestinal microecology and their association with altitude-related illness are poorly understood. Here, we used a rat model of hypobaric hypoxia challenge to mimic plateau exposure and monitored the gut microbiome, short-chain fatty acids (SCFAs), and bile acids (BAs) over 28 d. We identified weight loss, polycythemia, and pathological cardiac hypertrophy in hypoxic rats, accompanied by a large compositional shift in the gut microbiota, which is mainly driven by the bacterial families of Prevotellaceae, Porphyromonadaceae, and Streptococcaceae. The aberrant gut microbiota was characterized by increased abundance of the Parabacteroides, Alistipes, and Lactococcus genera and a larger Bacteroides to Prevotella ratio. Trans-omics analyses showed that the gut microbiome was significantly correlated with the metabolic abnormalities of SCFAs and BAs in feces, suggesting an interaction network remodeling of the microbiome-metabolome after the hypobaric hypoxia challenge. Interestingly, the transplantation of fecal microbiota significantly increased the diversity of the gut microbiota, partially inhibited the increased abundance of the Bacteroides and Alistipes genera, restored the decrease of plasma propionate, and moderately ameliorated cardiac hypertrophy in hypoxic rats. Our results provide an insight into the longitudinal changes in intestinal microecology during the hypobaric hypoxia challenge. Abnormalities in the gut microbiota and microbial metabolites contribute to the development of high-altitude heart disease in rats.

Rumen and fecal microbiota profiles associated with immunity of young and adult goats

Low immunity at birth increases risk of disease of young livestock, such as goat kids. Microbiomes change as animals mature, and a healthy microbiome is related to decreased risk of disease. The relationship between microbiota profiles and immunity at different developmental stages remains unclear. Young (female, n = 12, 30 d) and adult (female, n = 12, 2 yrs. old) Saanen dairy goats were used to investigate changes in rumen microbiomes, fecal microbiomes, and their correlations to circulating immune factors. Serum IgG (P = 0.02) and IgM (P < 0.01) were higher at 2 years than 30 d of age, but there were no differences in IgA (P = 0.34), IL-2 (P = 0.05), IL-4 (P = 0.37) and IL-6 (P = 0.73) between ages. Amplicon sequencing analysis revealed young goats had a higher diversity of bacterial communities in rumen and lower diversity in feces compared with adult goats. Ten genera in rumen and 14 genera in feces were positively correlated with serum IgM concentration across both ages. Olsenella, Methanosphaera, Quinella, Candidatus_Saccharimonas, and Methanobrevibacter in rumen and Ruminobacter, Treponema, Rikenelaceae_ RC9_ gut_ Group in feces were positively correlated with the concentration of IgG. The correlation analysis using weighted gene co-expression network analysis showed the MEblue module was positively associated with the IgG and IgM. These data provide novel insight into the association between rumen-feces microbiota and immune response. Further experiments are needed to investigate whether inoculating young livestock with immune-related bacteria identified can improve the immune status. Our data suggest a possible strategy to improve the immunity of the kids by alterative microbiota profiles.

Characterization of gut microbiota dysbiosis of diarrheic adult yaks through 16S rRNA gene sequences

The ruminant gut microbial community has a strong impact on host health and can be altered during diarrhea disease. As an indigenous breed of the Tibetan Plateau, domestic yak displays a high diarrhea rate, but little research has been done to characterize the bacterial microbial structure in diarrheic yaks. In the present study, a total of 30 adult yaks, assigned to diarrhea (case, N = 15) and healthy (control, N = 15) groups, were subjected to gut microbiota profiling using the V3–V4 regions of the 16S rRNA gene. The results showed that the gut microbiome of the case group had a significant decrease in alpha diversity. Additionally, differences in beta diversity were consistently observed for the case and control groups, indicating that the microbial community structure was changed due to diarrhea. Bacterial taxonomic analysis indicated that the Bacteroidetes, Firmicutes, and Proteobacteria were the three most dominant phyla in both groups but different in relative abundance. Especially, the proportion of Proteobacteria in the case group was increased as compared with the control group, whereas Spirochaetota and Firmicutes were significantly decreased. At the genus level, the relative abundance of Escherichia-Shigella and Prevotellaceae_UCG-003 were dramatically increased, whereas that of Treponema, p-2534-18B5_gut_group, and Prevotellaceae_UCG-001 were observably decreased with the effect of diarrhea. Furthermore, based on our linear discriminant analysis (LDA) effect size (LEfSe) results, Alistipes, Solibacillus, Bacteroides, Prevotellaceae_UCG_003, and Bacillus were significantly enriched in the case group, while the other five genera, such as Alloprevotella, RF39, Muribaculaceae, Treponema, and Enterococcus, were the most preponderant in the control group. In conclusion, alterations in gut microbiota community composition were associated with yak diarrhea, differentially represented bacterial species enriched in case animals providing a theoretical basis for establishing a prevention and treatment system for yak diarrhea.

Parturition and postpartum dietary change altered ruminal pH and the predicted functions of rumen bacterial communities but did not alter the bacterial composition in Holstein cows

We investigated the temporal dynamics of ruminal pH and the composition and predicted functions of the rumen bacterial community in Holstein cows during the periparturient period. Eight multiparous Holstein cows (body weight; 707.4 ± 29.9 kg, parity; 3.6 ± 0.6) were used for continuous reticulo-ruminal pH measurement, among which five were also used for bacterial community analysis. Rumen fluid samples were collected at 3 weeks before and 2 and 6 weeks after parturition, and blood samples were collected 3 weeks before and 0, 2, 4, and 6 weeks after parturition. After the parturition, reduction in the 1-h mean reticulo-ruminal pH was associated with a significant (P < 0.05) increase in total volatile fatty acid concentration. However, with the exception of a significant change in an unclassified genus of Prevotellaceae (P < 0.05), we detected no significant changes in the compositions of major bacterial phyla or genera or diversity indices during the periparturient period. On the basis of predicted functional analysis, we identified a total of 53 MetaCyc pathways (45 upregulated), 200 enzyme commissions (184 upregulated), and 714 Kyoto Encyclopedia of Genes and Genomes orthologs (667 upregulated) at 6 weeks postpartum that were significantly (P < 0.05) different to those at 3 weeks prepartum. Among the 14 MetaCyc pathways (P < 0.05) in which pyruvate is an end product, PWY-3661 [log2-fold change (FC) = 5.49, false discovery rate (FDR) corrected P < 0.001] was the most highly upregulated pyruvate-producing pathway. In addition, P381-PWY [adenosylcobalamin biosynthesis II (aerobic); FC = 5.48, FDR corrected P < 0.001] was the second most upregulated adenosylcobalamin (Vitamin B12)-producing pathway. In contrast, PWY-2221 (FC = −4.54, FDR corrected P = 0.003), predominantly found in pectinolytic bacteria, was the most downregulated pathway. Our findings indicate that changes in rumen bacterial community structure are not strictly associated with transitions in parturition or diet; however, we did observe changes in reticulo-ruminal pH and the metabolic adaptation of predicted functional pathways. Consequently, predictive analysis of postpartum functional pathways may enable us to gain insights into the underlying functional adaptations of bacterial communities in Holstein cows during the periparturient period.

Fresh Rumen Liquid Inoculant Enhances the Rumen Microbial Community Establishment in Pre-weaned Dairy Calves

The development of the functional rumen in calves involves a complex interplay between the host and host-related microbiome. Attempts to modulate rumen microbial community establishment may therefore have an impact on weaning success, calf health, and animal performance later in life. In this experiment, we aimed to elucidate how rumen liquid inoculum from an adult cow, provided to calves during the pre-weaning period, influences the establishment of rumen bacterial, archaeal, fungal, and ciliate protozoan communities in monozygotic twin calves (n = 6 pairs). The calves were divided into treatment (T-group) and control (C-group) groups, where the T-group received fresh rumen liquid as an oral inoculum during a 2-8-week period. The C-group was not inoculated. The rumen microbial community composition was determined using bacterial and archaeal 16S ribosomal RNA (rRNA) gene, protozoal 18S rRNA gene, and fungal ITS1 region amplicon sequencing. Animal weight gain and feed intake were monitored throughout the experiment. The T-group tended to have a higher concentrate intake (Treatment: p < 0.08) and had a significantly higher weekly weight gain (Treatment: p < 0.05), but no significant difference in volatile fatty acid concentrations between the groups was observed. In the T-group, the inoculum stimulated the earlier establishment of mature rumen-related bacterial taxa, affecting significant differences between the groups until 6 weeks of age. The inoculum also increased the archaeal operational taxonomic unit (OTU) diversity (Treatment: p < 0.05) but did not affect the archaeal quantity. Archaeal communities differed significantly between groups until week 4 (p = 0.02). Due to the inoculum, ciliate protozoa were detected in the T-group in week 2, while the C-group remained defaunated until 6 weeks of age. In week 8, Eremoplastron dilobum was the dominant ciliate protozoa in the C-group and Isotricha sp. in the T-group, respectively. The Shannon diversity of rumen anaerobic fungi reduced with age (Week: p < 0.01), and community establishment was influenced by a change of diet and potential interaction with other rumen microorganisms. Our results indicate that an adult cow rumen liquid inoculum enhanced the maturation of bacterial and archaeal communities in pre-weaning calves' rumen, whereas its effect on eukaryotic communities was less clear and requires further investigation.

ADDAGMA: A Database for Domestic Animal Gut Microbiome Atlas

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We curated all publicly available high-throughput sequencing data on gut microbiomes for four domestic animal species.

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We compiled data for multiple levels of microbial taxa and classified the associated animal phenotypes in detail.

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Exhibiting the dynamic changes of animal gut microbes under different conditions.

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We developed a user-friendly website for browsing, searching, and displaying dynamic changes in animal gut microbes under different conditions.

Animal gut microbiomes play important roles in the health, diseases, and production of animal hosts. The volume of animal gut metagenomic data, including both 16S amplicon and metagenomic sequencing data, has been increasing exponentially in recent years, making it increasingly difficult for researchers to query, retrieve, and reanalyze experimental data and explore new hypotheses. We designed a database called the domestic animal gut microbiome atlas (ADDAGMA) to house all publicly available, high-throughput sequencing data for the gut microbiome in domestic animals. ADDAGMA enhances the availability and accessibility of the rapidly growing body of metagenomic data. We annotated microbial and metadata from four domestic animals (cattle, horse, pig, and chicken) from 356 published papers to construct a comprehensive database that is equipped with browse and search functions, enabling users to make customized, complicated, biologically relevant queries. Users can quickly and accurately obtain experimental information on sample types, conditions, and sequencing platforms, and experimental results including microbial relative abundances, microbial taxon-associated host phenotype, and P-values for gut microbes of interest. The current version of ADDAGMA includes 290,422 quantification events (changes in abundance) for 3215 microbial taxa associated with 48 phenotypes. ADDAGMA presently covers gut microbiota sequencing data from pig, cattle, horse, and chicken, but will be expanded to include other domestic animals. ADDAGMA is freely available at (http://addagma.omicsbio.info/).

The rumen liquid metatranscriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula

Background

Targeted modification of the dairy calf ruminal microbiome has been attempted through rumen fluid inoculation to alter productive phenotypes later in life. However, sustainable effects of the early life interventions have not been well studied, particularly on the metabolically active rumen microbiota and its functions. This study investigated the sustained effects of adult-derived rumen fluid inoculations in pre-weaning dairy calves on the active ruminal microbiome of post-weaned dairy calves analyzed via RNA-sequencing.

Results

Two different adult-derived microbial inocula (bacterial- or protozoal-enriched rumen fluid; BE or PE, respectively) were administered in pre-weaned calves (3–6 weeks) followed by analyzing active rumen microbiome of post-weaned calves (9 weeks). The shared bacterial community at the genus level of 16S amplicon-seq and RNA-seq datasets was significantly different (P = 0.024), 21 out of 31 shared major bacterial genera differed in their relative abundance between the two analytic pipelines. No significant differences were found in any of the prokaryotic alpha- and beta-diversity measurements (P > 0.05), except the archaeota that differed for BE based on the Bray–Curtis dissimilarity matrix (P = 0.009). Even though the relative abundances of potentially transferred microbial and functional features from the inocula were minor, differentially abundant prokaryotic genera significantly correlated to various fermentation and animal measurements including butyrate proportion, body weight, and papillae length and counts. The overall microbial functions were affected quantitatively by BE and qualitatively by PE (P < 0.05), and this might be supported by the individual KEGG module and CAZymes profile differences. Exclusive networks between major active microbial (bacterial and archaeal genera) and functional features (KEGG modules) were determined which were differed by microbial inoculations.

Conclusions

This study demonstrated that actively transcribed microbial and functional features showed reliable connections with different fermentations and animal development responses through adult rumen fluid inoculations compared to our previous 16S amplicon sequencing results. Exclusive microbial and functional networks of the active rumen microbiome of dairy calves created by BE and PE might also be responsible for the different ruminal and animal characteristics. Further understanding of the other parts of the gastrointestinal tract (e.g., abomasum, omasum, and small intestine) using metatranscriptomics will be necessary to elucidate undetermined biological factors affected by microbial inoculations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00142-z.

Integrated Bacterial and Fungal Diversity Analysis Reveals the Gut Microbial Alterations in Diarrheic Giraffes

Gut microbiota has been demonstrated to be associated with multiple gastrointestinal diseases, but information regarding the gut microbial alternations in diarrheic giraffe remains scarce. Here, 16S rDNA and ITS gene amplicon sequencing were conducted to investigate the gut microbial composition and variability in diarrheic giraffes. Results demonstrated that Firmicutes and Proteobacteria were the most dominant phyla in the gut bacterial community, whereas Ascomycota and Basidiomycota were observed to be predominant in the gut fungal community regardless of health status. However, the species and relative abundance of preponderant bacterial and fungal genera in healthy and diarrheic giraffes were different. In contrast to the relatively stabilized gut fungal community, gut bacterial community displayed a significant decrease in the alpha diversity, accompanied by distinct changes in taxonomic compositions. Bacterial taxonomic analysis revealed that the relative abundances of eight phyla and 12 genera obviously increased, whereas the relative abundances of two phyla and eight genera dramatically decreased during diarrhea. Moreover, the relative richness of five fungal genera significantly increased, whereas the relative richness of seven fungal genera significantly declined in diarrheic giraffes. Taken together, this study demonstrated that diarrhea could cause significant alternations in the gut microbial composition of giraffes, and the changes in the gut bacterial community were more significant than those in the gut fungal community. Additionally, investigating the gut microbial characteristics of giraffes in different health states is beneficial to provide a theoretical basis for establishing a prevention and treatment system for diarrhea from the gut microbial perspective.

Rumen Fermentation, Digestive Enzyme Activity, and Bacteria Composition between Pre-Weaning and Post-Weaning Dairy Calves

Simple Summary

Weaning is very important for young ruminants. At this stage, calves’ main source of nutrients is transferred from milk into solid feed, such as starter and roughage. At the same time, the rumen function of calves undergoes tremendous changes, such as bacteria, which are the main players in rumen function. Our research found that the rumen bacteria network of post-weaning calves was more complex. The fermentation end products, such as acetate, propionate, and butyrate, were higher in the post-weaning calves than the pre-weaning group. However, digestive enzymes such as protease, carboxymethyl cellulase, cellobiohydrolase, and glucosidase were lower in the post-weaning calves than the pre-weaning calves. These findings provided useful information for reference regarding the feeding management of calves.

Abstract

To better understand the transition of rumen function during the weaning period in dairy calves, sixteen Holstein dairy calves were selected and divided into two groups: pre-weaning (age = 56 ± 7 day, n = 8) and post-weaning (age = 80 ± 6 day, n = 8). The rumen fluid was obtained by an oral gastric tube. The rumen fermentation profile, enzyme activity, bacteria composition, and their inter-relationship were investigated. The results indicated that the post-weaning calves had a higher rumen acetate, propionate, butyrate, and microbial crude protein (MCP) than the pre-weaning calves (p < 0.05). The rumen pH in the post-weaning calves was lower than the pre-weaning calves (p < 0.05). The protease, carboxymethyl cellulase, cellobiohydrolase, and glucosidase in the post-weaning calves had a lower trend than the pre-weaning calves (0.05 < p < 0.1). There was no difference in α and β diversity between the two groups. Linear discriminant analysis showed that the phylum of Fibrobacteres in the post-weaning group was higher than the pre-weaning group. At the genus level, Shuttleworthia, Rikenellaceae, Fibrobacter, and Syntrophococcus could be worked as the unique bacteria in the post-weaning group. The rumen bacteria network node degree in the post-weaning group was higher than the pre-weaning group (16.54 vs. 9.5). The Shuttleworthia genus was highly positively correlated with MCP, propionate, total volatile fatty acid, glucosidase, acetate, and butyrate (r > 0.65, and p < 0.01). Our study provided new information about the rumen enzyme activity and its relationship with bacteria, which help us to better understand the effects of weaning on the rumen function.

Microbial colonization of the gastrointestinal tract of dairy calves - a review of its importance and relationship to health and performance

This review aims to explain how microbial colonization of the gastrointestinal tract (GIT) in young dairy calves is related to health and, consequently, to the performance of these animals. The review addresses everything from the fundamental aspects of microbial colonization to the current understanding about the microbiota manipulation to improve performance in adult animals. The ruminal microbiota is the most studied, mainly due to the high interest in the fermentative aspects, the production of short-chain fatty acids, and microbial proteins, and its effects on animal production. However, in recent years, the intestinal microbiota has gained space between studies, mainly due to the relationship to the host health and how it affects performance. Understanding how the GIT's microbiota looks like and how it is colonized may allow future studies to predict the best timing for dietary interventions as a way to manipulate it and, consequently, improve the health and performance of young ruminants.

Pre-weaning Ruminal Administration of Differentially-Enriched, Rumen-Derived Inocula Shaped Rumen Bacterial Communities and Co-occurrence Networks of Post-weaned Dairy Calves

Adult rumen fluid inoculations have been considered to facilitate the establishment of rumen microbiota of pre-weaned dairy calves. However, the sustained effects of the inoculations remain to be explored. In our previous study, 20 pre-weaned dairy calves had been dosed with four types of adult rumen inoculums [autoclaved rumen fluid, bacterial-enriched rumen fluid (BE), protozoal-enriched (PE), and BE + PE] weekly at 3 to 6 weeks of age. To verify the sustained effect of adult rumen inoculation, the rumen bacterial communities, fermentation characteristics, and animal performance measurements were measured after sacrifice from 20 post-weaned dairy bull calves (9 weeks of age). Ruminal pH tended to be lower in BE treated calves (n = 10). All PE treated calves had rumen ciliates (>104 cells per ml of rumen fluid). PE treated calves had greater VFA concentrations (P = 0.052), lower molar proportions of isobutyrate (P = 0.073), and butyrate (P = 0.019) compared to those of control calves. No treatment differences were found in all animal performance measurements. Both PE and BE inocula increased bacterial species richness, Faith's phylogenetic diversity, and Shannon's index in rumen liquid fractions. However, the relative proportion of those bacterial taxa possibly transferred from the donor's rumen was minor. Microbial network analysis showed different co-occurrence and mutually exclusive interactions between treatments of microbial inoculations. Collectively, adult rumen inoculations in pre-weaned dairy calves slightly altered the rumen bacteriome of post-weaned calves without changing fermentation and animal performance.

Dynamic progression of the calf's microbiome and its influence on host health

The first year of a calf's life is a critical phase as its digestive system and immunity are underdeveloped. A high level of stress caused by separation from mothers, transportation, antibiotic treatments, dietary shifts, and weaning can have long-lasting health effects, which can reduce future production parameters, such as milk yield and reproduction, or even increase the mortality of calves. The early succession of microbes throughout the gastrointestinal tract of neonatal calves follows a sequential pattern of colonisation and is greatly influenced by their physiological state, age, diet, and environmental factors; this leads to the establishment of region- and site-specific microbial communities. This review summarises the current information on the various potential factors that may affect the early life microbial colonisation pattern in the gastrointestinal tract of calves. The possible role of host-microbe interactions in the development and maturation of host gut, immune system, and health are described. Additionally, the possibility of improving the health of calves through gut microbiome modulation and using antimicrobial alternatives is discussed. Finally, the trends, challenges, and limitations of the current research are summarised and prospective directions for future studies are highlighted.