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

Abstract 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.

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PSV-16 Influence of the late gestation maternal rumen microbiome on the calf meconium and early rumen microbiome

Journal of Animal Science ◽

10.1093/jas/skaa054.290 ◽

2020 ◽

Vol 98 (Supplement_3) ◽

pp. 164-164

Author(s):

Kelly Woodruff ◽

Gwendolynn Hummel ◽

Kathleen Austin ◽

Travis Smith ◽

Hannah Cunningham-Hollinger

Keyword(s):

Beta Diversity ◽

Rumen Fluid ◽

Amplicon Sequencing ◽

Late Gestation ◽

Sample Type ◽

Alpha And Beta Diversity ◽

Rumen Microbiome ◽

Beef Herd ◽

The University ◽

Microbial Dna

Abstract Understanding the development of the calf rumen microbiome is important in developing manipulation strategies to improve efficiency as the animal ages. We hypothesized that the cow maternal microbiome would influence the colonization of the calf rumen microbiome. Our objective was to relate the microbiomes of the cow rumen fluid (RFC) to the calf meconium (M) and calf rumen fluid (RFN) at twenty-eight days of age. Mature, multiparous Angus crossbred cows (n = 10) from the University of Wyoming beef herd were used in this study. Rumen fluid was collected from the cows prior to parturition. Immediately following parturition, meconium was collected from the calf and at 28 days post-parturition, rumen fluid was collected from the calves. Microbial DNA was isolated using a lysis buffer and mechanical bead-beating procedure and purified using the QIAamp DNA Stool Mini Kit (Qiagen). Amplicon sequencing of the 16S rRNA V4 region was completed on the MiSeq and analyzed with QIIME2. Both alpha and beta diversity were evaluated by sample type and day. Richness and evenness differed by sample type. The greatest richness and evenness was in RFC (q < 0.01) followed by RFN and M, which did not differ from each other (q ³ 0.5). Bray-Curtis and Jaccard beta diversity differed by each sample type (q < 0.01). These data indicate that the M and RFN do not differ in number and distribution of features, but the samples are compositionally different. Additionally, the RFC differed in both alpha and beta diversity from both calf samples. These profiles can be used to develop hypotheses for the pathway of colonization in the early gut yet still reflect the vast differences in the developmental stage between the cow rumen microbiome and the early calf gastrointestinal microbiome.

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Early life dietary intervention in dairy calves results in a long-term reduction in methane emissions

Scientific Reports ◽

10.1038/s41598-021-82084-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

S. J. Meale ◽

M. Popova ◽

C. Saro ◽

C. Martin ◽

A. Bernard ◽

...

Keyword(s):

Methane Production ◽

Dietary Intervention ◽

Rumen Fluid ◽

Methane Emissions ◽

Microbial Colonization ◽

Dairy Calves ◽

Rumen Microbes ◽

Rumen Microbiome ◽

Fungal Structure

AbstractRecent evidence suggests that changes in microbial colonization of the rumen prior to weaning may imprint the rumen microbiome and impact phenotypes later in life. We investigated how dietary manipulation from birth influences growth, methane production, and gastrointestinal microbial ecology. At birth, 18 female Holstein and Montbéliarde calves were randomly assigned to either treatment or control (CONT). Treatment was 3-nitrooxypropanol (3-NOP), an investigational anti-methanogenic compound that was administered daily from birth until three weeks post-weaning (week 14). Samples of rumen fluid and faecal content were collected at weeks 1, 4, 11, 14, 23, and 60 of life. Calves were tested for methane emissions using the GreenFeed system during the post-weaning period (week 11–23 and week 56–60 of life). Calf physiological parameters (BW, ADG and individual VFA) were similar across groups throughout the trial. Treated calves showed a persistent reduction in methane emissions (g CH4/d) throughout the post-weaning period up to at least 1 year of life, despite treatment ceasing three weeks post-weaning. Similarly, despite variability in the abundance of individual taxa across weeks, the rumen bacterial, archaeal and fungal structure differed between CONT and 3-NOP calves across all weeks, as visualised using sparse-PLS-DA. Similar separation was also observed in the faecal bacterial community. Interestingly, despite modest modifications to the abundance of rumen microbes, the reductive effect of 3-NOP on methane production persisted following cessation of the treatment period, perhaps indicating a differentiation of the ruminal microbial ecosystem or a host response triggered by the treatment in the early development phase.

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269 Influence of the maternal rumen microbiome on development of the calf meconium and rumen microbiome

Journal of Animal Science ◽

10.1093/jas/skaa278.359 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 195-195

Author(s):

Kelly Woodruff ◽

Gwendolynn Hummel ◽

Kathleen Austin ◽

Travis Smith ◽

Hannah Cunningham

Keyword(s):

Beta Diversity ◽

Management Practices ◽

Sequence Data ◽

Rumen Fluid ◽

Alpha Diversity ◽

Illumina Miseq ◽

Sample Type ◽

Microbial Composition ◽

Alpha And Beta Diversity ◽

Rumen Microbiome

Abstract Optimization of host performance may be achieved through programming of the rumen microbiome. Thus, understanding maternal influences on the development of the calf rumen microbiome is critical. We hypothesized that the cow maternal rumen microbiome would influence colonization of the calf rumen microbiome. Our objective was to relate the microbiome of the cow rumen fluid prior to parturition (RFC) and at weaning (RFCw) to the calf’s meconium microbiome (M) and calf rumen fluid microbiome at birth (RFd1), d 2 (RFd2), d 28 (RFd28), and weaning (RFNw). Multiparous Angus crossbred cows (n = 10) from the University of Wyoming beef herd were used. Rumen fluid was collected from the cows prior to parturition and at weaning. Immediately following parturition, meconium and rumen fluid were collected from the calf. Rumen fluid was collected again at d 2, 28, and at weaning. Microbial DNA was isolated and 16S rRNA sequencing was completed on the Illumina MiSeq. Sequence data were analyzed with QIIME2 to determine both alpha and beta diversity by sample type and day. Alpha diversity metrics reported similarities in the early gut microbiome (M, RFd1, and RFD2; q ≥ 0.12) and between the cow and calf at weaning (q ≥ 0.06). Microbial composition as determined by beta diversity differed in the early rumen microbiome (RFd1, RFd2, and RFd28; q ≤ 0.04). There were similarities in composition between M, RFCw, and RFd1 (q ≥ 0.09). These data can be used to develop hypotheses for the pathway of colonization in the early gut and can provide insight into management practices affecting the microbiome, improving host performance.

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Retinitis pigmentosa is associated with shifts in the gut microbiome

Scientific Reports ◽

10.1038/s41598-021-86052-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Oksana Kutsyr ◽

Lucía Maestre-Carballa ◽

Mónica Lluesma-Gomez ◽

Manuel Martinez-Garcia ◽

Nicolás Cuenca ◽

...

Keyword(s):

Retinitis Pigmentosa ◽

Gut Microbiome ◽

Functional Decline ◽

Retinal Disease ◽

Photoreceptor Cells ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequencing Data ◽

Alpha And Beta Diversity ◽

Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

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Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

Scientific Reports ◽

10.1038/s41598-021-91615-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kazutoshi Yoshitake ◽

Gaku Kimura ◽

Tomoko Sakami ◽

Tsuyoshi Watanabe ◽

Yukiko Taniuchi ◽

...

Keyword(s):

Time Series ◽

Microbial Communities ◽

Pacific Coast ◽

Three Dimensional ◽

Amplicon Sequencing ◽

Metagenomic Data ◽

Shotgun Metagenomics ◽

Functional Features ◽

Pacific Coast Of Japan ◽

Marine Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

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SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

Scientific Reports ◽

10.1038/s41598-021-88536-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tzipi Braun ◽

Shiraz Halevi ◽

Rotem Hadar ◽

Gilate Efroni ◽

Efrat Glick Saar ◽

...

Keyword(s):

Clinical Microbiology ◽

Amplicon Sequencing ◽

Viral Disease ◽

Nasopharyngeal Swab ◽

Microbial Composition ◽

16S Amplicon Sequencing ◽

The World ◽

Health And Disease ◽

Longitudinal Sampling ◽

Potential Interactions

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

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Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function

BMC Genomics ◽

10.1186/s12864-020-07307-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gongchao Jing ◽

Yufeng Zhang ◽

Wenzhi Cui ◽

Lu Liu ◽

Jian Xu ◽

...

Keyword(s):

16S Rrna ◽

Large Scale ◽

Low Cost ◽

Human Microbiome ◽

Amplicon Sequencing ◽

Training Sample ◽

Rrna Gene ◽

16S Amplicon Sequencing ◽

Cross Platform ◽

Functional Profiles

Abstract Background Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. Results Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. Conclusions This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

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PSVI-22 Rumen microbiome of beef cattle is modulated by backgrounding systems

Journal of Animal Science ◽

10.1093/jas/skaa054.383 ◽

2020 ◽

Vol 98 (Supplement_3) ◽

pp. 220-220

Author(s):

Bobwealth O Omontese ◽

Ashok K Sharma ◽

Jason Langlie ◽

Joe Armstrong ◽

Alfredo DiCostanzo ◽

...

Keyword(s):

Beef Cattle ◽

Developmental Stages ◽

Production Systems ◽

Rumen Fluid ◽

Illumina Miseq ◽

High Energy ◽

Shannon Index ◽

Bacterial Gene ◽

Beef Calves ◽

Rumen Microbiome

Abstract Backgrounding (BKG) segment in beef production systems is characterized by utilization of different forages which affect growth performance and carcass characteristics. However, it is unclear how BKG systems impact rumen microbiome. We investigated rumen microbiome dynamics of beef calves under different BKG systems. At weaning, Angus and Angus x Simmental beef calves (n = 38) were stratified by age, weight, and sex in a completely randomized design into 1 of 3 BKG treatments for 55 d: 1) perennial pasture (PP; quackgrass, orchardgrass; smooth bromegrass, red clover, and alfalfa); 2) summer annual cover crop (CC; cereal oats, purple top turnips, hunter forage brassica, and graza forage radish); and 3) dry lot (DL; haylage, corn, and DDGS). After BKG, all calves were assigned to a high energy ration in a feedlot. Rumen sample was collected via esophageal tubing at weaning, BKG and feedlot. A total of 190 rumen fluid samples were used to sequence the hypervariable V4 region of the 16S rRNA bacterial gene on an Illumina MiSeq platform. The results showed that BKG systems largely influenced rumen bacterial communities. Specifically, microbiome composition and diversity were not different at weaning, diverged significantly during BKG (Shannon index, Bray Curtis distance metrics; P < 0.001) and homogenized during feedlot. During the BKG segment, the bacterial genera Agrobacterium, Coprococcus, and Ruminococcus were dominant in CC whereas Fibrobacteraceae and Mycoplasmataceae was most dominant in DL. Moreover, rumen microbiome patterns of CC and DL calves showed increased plasticity in early stages of development but not during feedlot with PP showing fewer changes over time. These results indicate that BKG systems significantly modulate the rumen microbiome of beef cattle and, underscore the importance of early developmental stages as potential targets for feeding interventions that can impact the animal microbiome to enhance animal performance.

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131 Can Maternal Nutrition in Dairy Cattle Impact Gut Health in Dairy Calves?

Journal of Animal Science ◽

10.1093/jas/skab235.126 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 69-70

Author(s):

Lautaro Rostoll Cangiano ◽

Nilusha Malmuthuge ◽

Tao Ma ◽

Leluo Guan ◽

Michael A Steele

Keyword(s):

Developmental Plasticity ◽

Maternal Nutrition ◽

Critical Role ◽

Dairy Calves ◽

Milk Replacer ◽

Gastrointestinal Function ◽

Dairy Calf ◽

Gastrointestinal Health ◽

Nutrition Research ◽

Pregnancy And Postpartum

Abstract The nutritional management, health and welfare of the dairy calf has historically received less attention due to limited research, and recommendations largely focused on passive transfer of immunity and early weaning strategies. Gastrointestinal diseases and disorders remain the leading cause of mortality and morbidity in dairy calves worldwide. Despite the recent thrust in dairy calf nutrition research, major knowledge gaps still exist regarding how maternal nutrition during pregnancy and postpartum impact gastrointestinal health and function, especially during the fetal and neonatal stages when the developmental plasticity is highest. Recent research has focused on how prepartum nutrition and management can influence colostrum quality and has characterized numerous bioactive proteins, lipids, and carbohydrates that may play a critical role in gastrointestinal function and development. It has also been shown that colostrum plays a fundamental role in promoting colonization with commensal bacteria; however, delaying colostrum feeding or abruptly transitioning calves from colostrum to milk decreased the colonization of beneficial bacteria and impaired gastrointestinal development. With respect to the maternal nutrient supply via milk, it is important to note that calves have been traditionally fed less than half of voluntary intake or fed milk replacer formulations that can largely differ in composition from that of maternal milk. Recent research indicated that common milk replacer formulations may impair gastrointestinal function, highlighting the need to question existing nutritional regimens. In addition, feeding prophylactic antibiotics in milk, as well as waste milk containing antibiotic residues, are common practices in the dairy industry, despite recent studies reporting that these practices can increase calf susceptibility to infections by disrupting gut microbiome and gut function. Although our knowledge how maternal factors impact the gastrointestinal tract of calves is limited, it is clear there are great opportunities to further develop prenatal and postnatal nutritional programs to improve dairy calf gastrointestinal health.

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Obtaining Various Shapes of Machined Surface Using a Tool with a Multi-Insert Cutting Edge

Applied Sciences ◽

10.3390/app9050880 ◽

2019 ◽

Vol 9 (5) ◽

pp. 880 ◽

Cited By ~ 1

Author(s):

Tadeusz Mikolajczyk ◽

Danil Pimenov ◽

Catalin Pruncu ◽

Karali Patra ◽

Hubert Latos ◽

...

Keyword(s):

Cutting Edge ◽

Machined Surface ◽

Wide Range ◽

Complex Shapes ◽

Functional Features ◽

Tool Set ◽

The Individual ◽

Milling Tools ◽

Novel Design ◽

Positive Results

A novel design of a universal form tool is presented for machining complex planar and axisymmetric surfaces. The geometric and kinematic flexibility (GKF) of this tool type means that it can machine a wide range of profiles using a single setup. The operating principle of this multi-insert tool is its combination of single cutting edges, each of which form the individual details of the machined surface. The structure and application of both turning and milling multi-insert tools with combinations of single edges are described in the paper. Complex shapes and forms can be machined by changing the cutting-edge positions. The number of combinations of a given tool set can be determined by using the relations detailed in this study. Both turning and milling tools are utilized in a unique tool holder that clamps the inserts into position and allows their adjustment that is facilitated by special prepared analytical software to the desired object profiles. It is possible to use these tools in machining both wood and aluminum alloys. Finally, the design of the multi-insert tools for turning and milling and its functional features were experimentally verified with positive results.

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