Publications by authors named "Garret Suen"

95 Publications

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers.

J Anim Sci Biotechnol 2021 Jul 15;12(1):79. Epub 2021 Jul 15.

Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.

Background: Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients. However, little is known about the association between the rumen microbiota and feed efficiency traits in Nellore (Bos indicus) cattle, a breed of major economic importance to the global beef market. Here, we compare the composition of the bacterial, archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency (FE) phenotypes, as measured by residual feed intake (RFI).

Results: The Firmicutes to Bacteroidetes ratio was significantly higher (P < 0.05) in positive-RFI steers (p-RFI, low feed efficiency) than in negative-RFI (n-RFI, high feed efficiency) steers. The differences in bacterial composition from steers with high and low FE were mainly associated with members of the families Lachnospiraceae, Ruminococcaceae and Christensenellaceae, as well as the genus Prevotella. Archaeal community richness was lower (P < 0.05) in p-RFI than in n-RFI steers and the genus Methanobrevibacter was either increased or exclusive of p-RFI steers. The fungal genus Buwchfawromyces was more abundant in the rumen solid fraction of n-RFI steers (P < 0.05) and a highly abundant OTU belonging to the genus Piromyces was also increased in the rumen microbiota of high-efficiency steers. However, analysis of rumen fermentation variables and functional predictions indicated similar metabolic outputs for the microbiota of distinct FE groups.

Conclusions: Our results demonstrate that differences in the ruminal microbiota of high and low FE Nellore steers comprise specific taxa from the bacterial, archaeal and fungal communities. Biomarker OTUs belonging to the genus Piromyces were identified in animals showing high feed efficiency, whereas among archaea, Methanobrevibacter was associated with steers classified as p-RFI. The identification of specific RFI-associated microorganisms in Nellore steers could guide further studies targeting the isolation and functional characterization of rumen microbes potentially important for the energy-harvesting efficiency of ruminants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40104-021-00599-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8281616PMC
July 2021

Assessing the Response of Ruminal Bacterial and Fungal Microbiota to Whole-Rumen Contents Exchange in Dairy Cows.

Front Microbiol 2021 1;12:665776. Epub 2021 Jun 1.

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.

A major goal for the dairy industry is to improve overall milk production efficiency (MPE). With the advent of next-generation sequencing and advanced methods for characterizing microbial communities, efforts are underway to improve MPE by manipulating the rumen microbiome. Our previous work demonstrated that a near-total exchange of whole rumen contents between pairs of lactating Holstein dairy cows of disparate MPE resulted in a reversal of MPE status for ∼10 days: historically high-efficiency cows decreased in MPE, and historically low-efficiency cows increased in MPE. Importantly, this switch in MPE status was concomitant with a reversal in the ruminal bacterial microbiota, with the newly exchanged bacterial communities reverting to their pre-exchange state. However, this work did not include an in-depth analysis of the microbial community response or an interrogation of specific taxa correlating to production metrics. Here, we sought to better understand the response of rumen communities to this exchange protocol, including consideration of the rumen fungi. Rumen samples were collected from 8 days prior to, and 56 days following the exchange and were subjected to 16S rRNA and ITS amplicon sequencing to assess bacterial and fungal community composition, respectively. Our results show that the ruminal fungal community did not differ significantly between hosts of disparate efficiency prior to the exchange, and no change in community structure was observed over the time course. Correlation of microbial taxa to production metrics identified one fungal operational taxonomic unit (OTU) in the genus that correlated positively to MPE, and several bacterial OTUs classified to the genus . Within the , was found to be more abundant in high-efficiency cows whereas was more abundant in low-efficiency cows. Overall, our results suggest that the rumen bacterial community is a primary microbial driver of host efficiency, that the ruminal fungi may not have as significant a role in MPE as previously thought, and that more work is needed to better understand the functional roles of specific ruminal microbial community members in modulating MPE.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.665776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8203821PMC
June 2021

The Rumen Bacterial Community in Dairy Cows Is Correlated to Production Traits During Freshening Period.

Front Microbiol 2021 4;12:630605. Epub 2021 Mar 4.

State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China.

The rumen microbiome plays a vital role in providing nutrition to the host animal, thereby influencing ruminant production. Despite its importance, it is not fully understood how variation in the ruminal bacteria community composition influences dry matter intake (DMI), milk yield and ruminal fermentative parameters in dairy cows, especially during freshening period. Here, we hypothesized that during early lactation, high DMI cows having a different ruminal microbiota than low DMI cows, and that this difference persists over time. To test this, we enrolled 65 fresh and determinzed their DMI using an auto-feed intake recording system. Fourteen days after calving, the 10 animals with the lowest (LFI) and the 10 animals with the highest (HFI)-average DMI were selected for further analysis. Rumen fluid was collected from these two cohorts at 1 (Fresh1d) and 14 days (Fresh14d) after calving and their ruminal microbiota were assessed using 16S rRNA sequencing. Volatile fatty acid (VFA) concentrations were also quantified. Comparison of the ruminal microbiotas between Fresh1d and Fresh14d showed that Fresh14d cows had a significantly higher relative abundance of VFA-producing microbes ( < 0.05), such as and . This was commensurate with the concentrations of acetate, propionate, butyrate, valerate and total VFAs, were also significantly ( < 0.05) increased in Fresh14d cows. We also found that the differences in the ruminal microbiota between LFI and HFI cows was limited, but DMI significantly altered ( < 0.05) the relative proportion of bacteria in the families , and . Furthermore, specific operational taxonomic units belonging to the was significantly ( < 0.05) correlated with DMI and milk yield. Taking together, our findings provide a framework for future studies of freshening period cow that seek to better understand the role of the ruminal microbiota during this critical period in the lactation cycle.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.630605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7969525PMC
March 2021

Multiomics analysis reveals the presence of a microbiome in the gut of fetal lambs.

Gut 2021 May 15;70(5):853-864. Epub 2021 Feb 15.

Feed Research Institute, Chinese Academy of Agricultural Sciences, National Engineering Research Center of Biological Feed, Beijing, China

Objective: Microbial exposure is critical to neonatal and infant development, growth and immunity. However, whether a microbiome is present in the fetal gut prior to birth remains debated. In this study, lambs delivered by aseptic hysterectomy at full term were used as an animal model to investigate the presence of a microbiome in the prenatal gut using a multiomics approach.

Design: Lambs were euthanised immediately after aseptic caesarean section and their cecal content and umbilical cord blood samples were aseptically acquired. Cecal content samples were assessed using metagenomic and metatranscriptomic sequencing to characterise any existing microbiome. Both sample types were analysed using metabolomics in order to detect microbial metabolites.

Results: We detected a low-diversity and low-biomass microbiome in the prenatal fetal gut, which was mainly composed of bacteria belonging to the phyla Proteobacteria, Actinobacteria and Firmicutes. was the most abundant species in the prenatal fetal gut. We also detected multiple microbial metabolites including short chain fatty acids, deoxynojirimycin, mitomycin and tobramycin, further indicating the presence of metabolically active microbiota. Additionally, bacteriophage phiX174 and Orf virus, as well as antibiotic resistance genes, were detected in the fetal gut, suggesting that bacteriophage, viruses and bacteria carrying antibiotic resistance genes can be transmitted from the mother to the fetus during the gestation period.

Conclusions: This study provides strong evidence that the prenatal gut harbours a microbiome and that microbial colonisation of the fetal gut commences in utero.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/gutjnl-2020-320951DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040156PMC
May 2021

A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone.

Nat Commun 2021 02 3;12(1):763. Epub 2021 Feb 3.

Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.

Human and animal infections with bacteria of the genus Sarcina (family Clostridiaceae) are associated with gastric dilation and emphysematous gastritis. However, the potential roles of sarcinae as commensals or pathogens remain unclear. Here, we investigate a lethal disease of unknown etiology that affects sanctuary chimpanzees (Pan troglodytes verus) in Sierra Leone. The disease, which we have named "epizootic neurologic and gastroenteric syndrome" (ENGS), is characterized by neurologic and gastrointestinal signs and results in death of the animals, even after medical treatment. Using a case-control study design, we show that ENGS is strongly associated with Sarcina infection. The microorganism is distinct from Sarcina ventriculi and other known members of its genus, based on bacterial morphology and growth characteristics. Whole-genome sequencing confirms this distinction and reveals the presence of genetic features that may account for the unusual virulence of the bacterium. Therefore, we propose that this organism be considered the representative of a new species, named "Candidatus Sarcina troglodytae". Our results suggest that a heretofore unrecognized complex of related sarcinae likely exists, some of which may be highly virulent. However, the potential role of "Ca. S. troglodytae" in the etiology of ENGS, alone or in combination with other factors, remains a topic for future research.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-021-21012-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859188PMC
February 2021

Editorial: Gut Microbiome Modulation in Ruminants: Enhancing Advantages and Minimizing Drawbacks.

Front Microbiol 2020 11;11:622002. Epub 2021 Jan 11.

Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.622002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7829182PMC
January 2021

Multiplexed Competition in a Synthetic Squid Light Organ Microbiome Using Barcode-Tagged Gene Deletions.

mSystems 2020 Dec 15;5(6). Epub 2020 Dec 15.

Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA

Beneficial symbioses between microbes and their eukaryotic hosts are ubiquitous and have widespread impacts on host health and development. The binary symbiosis between the bioluminescent bacterium and its squid host serves as a model system to study molecular mechanisms at the microbe-animal interface. To identify colonization factors in this system, our lab previously conducted a global transposon insertion sequencing (INSeq) screen and identified over 300 putative novel squid colonization factors in To pursue mechanistic studies on these candidate genes, we present an approach to quickly generate barcode-tagged gene deletions and perform high-throughput squid competition experiments with detection of the proportion of each strain in the mixture by barcode sequencing (BarSeq). Our deletion approach improves on previous techniques based on splicing by overlap extension PCR (SOE-PCR) and -based natural transformation by incorporating a randomized barcode that results in unique DNA sequences within each deletion scar. Amplicon sequencing of the pool of barcoded strains before and after colonization faithfully reports on known colonization factors and provides increased sensitivity over colony counting methods. BarSeq enables rapid and sensitive characterization of the molecular factors involved in establishing the -squid symbiosis and provides a valuable tool to interrogate the molecular dialogue at microbe-animal host interfaces. Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Model symbioses are therefore invaluable for studying the mechanisms of beneficial microbe-host interactions. Here, we present a combined barcode-tagged deletion and BarSeq approach to interrogate the molecular dialogue that ensures specific and reproducible colonization of the Hawaiian bobtail squid by The ability to precisely manipulate the bacterial genome, combined with multiplex colonization assays, will accelerate the use of this valuable model system for mechanistic studies of how environmental microbes-both beneficial and pathogenic-colonize specific animal hosts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSystems.00846-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7771539PMC
December 2020

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.

Nat Commun 2020 12 15;11(1):6389. Epub 2020 Dec 15.

ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.

Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-19929-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7738495PMC
December 2020

Use of a systems engineering framework to assess perceptions and practices about antimicrobial resistance of workers on large dairy farms in Wisconsin.

medRxiv 2020 Nov 3. Epub 2020 Nov 3.

We studied farmworker practices potentially contributing to transmission of bacteria and antimicrobial resistant genes (ARGs) among animals and farm workers to identify human behavioral interventions to reduce exposure risk. Ten focus groups were conducted on eight farms to explore potentially high-risk practices and farmworker knowledge and experiences with antimicrobial use and resistance using the Systems Engineering in Patient Safety (SEIPS) framework. Farmworkers were asked to describe common tasks and the policies guiding these practices. We found workers demonstrated knowledge of the role of antibiotic stewardship in preventing the spread of ARGs. Knowledge of various forms of personal protective equipment was higher for workers who commonly reported glove-use. Knowledge regarding the importance of reducing ARG transmission varied but was greater than previously reported. Programs to reduce ARG spread on dairy farms should focus on proper hand hygiene and personal protective equipment use but at the level of knowledge, beliefs, and practices.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1101/2020.10.28.20221747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7654902PMC
November 2020

Assessing the Beneficial Effects of the Immunomodulatory Glycan LNFPIII on Gut Microbiota and Health in a Mouse Model of Gulf War Illness.

Int J Environ Res Public Health 2020 09 27;17(19). Epub 2020 Sep 27.

Department of Physiology and Pharmacology, University of Georgia, Athens, GA 30602, USA.

The microbiota's influence on host (patho) physiology has gained interest in the context of Gulf War Illness (GWI), a chronic disorder featuring dysregulation of the gut-brain-immune axis. This study examined short- and long-term effects of GWI-related chemicals on gut health and fecal microbiota and the potential benefits of Lacto-N-fucopentaose-III (LNFPIII) treatment in a GWI model. Male C57BL/6J mice were administered pyridostigmine bromide (PB; 0.7 mg/kg) and permethrin (PM; 200 mg/kg) for 10 days with concurrent LNFPIII treatment (35 μg/mouse) in a short-term study (12 days total) and delayed LNFPIII treatment (2×/week) beginning 4 months after 10 days of PB/PM exposure in a long-term study (9 months total). Fecal 16S rRNA sequencing was performed on all samples post-LNFPIII treatment to assess microbiota effects of GWI chemicals and acute/delayed LNFPIII administration. Although PB/PM did not affect species composition on a global scale, it affected specific taxa in both short- and long-term settings. PB/PM elicited more prominent long-term effects, notably, on the abundances of bacteria belonging to and families and the genus . LNFPIII improved a marker of gut health (i.e., decreased lipocalin-2) independent of GWI and, importantly, increased butyrate producers (e.g., , ) in PB/PM-treated mice, indicating a positive selection pressure for these bacteria. Multiple operational taxonomic units correlated with aberrant behavior and lipocalin-2 in PB/PM samples; LNFPIII was modulatory. Overall, significant and lasting GWI effects occurred on specific microbiota and LNFPIII treatment was beneficial.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijerph17197081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7579323PMC
September 2020

Ruminal Fermentation Pattern, Bacterial Community Composition, and Nutrient Digestibility of Nellore Cattle Submitted to Either Nutritional Restriction or Intake of Concentrate Feedstuffs Prior to Adaptation Period.

Front Microbiol 2020 31;11:1865. Epub 2020 Jul 31.

College of Technology and Agricultural Sciences, São Paulo State University (UNESP), Dracena, Brazil.

Beef cattle are key contributors to meat production and represent critical drivers of the global agricultural economy. In Brazil, beef cattle are reared in tropical pastures and finished in feedlot systems. The introduction of cattle into a feedlot includes a period where they adapt to high-concentrate diets. This adaptation period is critical to the success of incoming cattle, as they must adjust to both a new diet and environment. Incoming animals are typically reared on a variety of diets, ranging from poor quality grasses to grazing systems supplemented with concentrate feedstuffs. These disparate pre-adaptation diets present a challenge, and here, we sought to understand this process by evaluating the adaptation of Nellore calves raised on either grazing on poor quality grasses (restriction diet) or grazing systems supplemented with concentrate (concentrate diet). Given that nutrient provisioning from the diet is the sole responsibility of the ruminal microbial community, we measured the impact of this dietary shift on feeding behavior, ruminal fermentation pattern, ruminal bacterial community composition (BCC), and total tract digestibility. Six cannulated Nellore bulls were randomly assigned to two 3 × 3 Latin squares, and received a control, restriction, or concentrate diet. All cohorts were then fed the same adaptation diet to mimic a standard feedlot. Ruminal BCC was determined using Illumina-based 16S rRNA amplicon community sequencing. We found that concentrate-fed cattle had greater dry matter intake ( < 0.01) than restricted animals. Likewise, cattle fed concentrate had greater ( = 0.02) propionate concentration during the adaptation phase than control animals and a lower Shannon's diversity ( = 0.02), relative to the restricted animals. We also found that these animals had lower ( = 0.04) relative abundances of when compared to control animals during the pre-adaptation phase and lower abundances of bacteria within the during the finishing phase, when compared to the control animals ( = 0.05). Finally, we found that animals previously exposed to concentrate were able to better adapt to high-concentrate diets when compared to restricted animals. Our study presents the first investigation of the impact of pre-adaptation diet on ruminal BCC and metabolism of bulls during the adaptation period. We suggest that these results may be useful for planning adaptation protocols of bulls entering the feedlot system and thereby improve animal production.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.01865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7412545PMC
July 2020

Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach.

Appl Environ Microbiol 2020 08 18;86(17). Epub 2020 Aug 18.

US Dairy Forage Research Center, USDA-Agricultural Research Service, Madison, Wisconsin, USA

Analysis of the cow microbiome, as well as host genetic influences on the establishment and colonization of the rumen microbiota, is critical for development of strategies to manipulate ruminal function toward more efficient and environmentally friendly milk production. To this end, the development and validation of noninvasive methods to sample the rumen microbiota at a large scale are required. In this study, we further optimized the analysis of buccal swab samples as a proxy for direct bacterial samples of the rumen of dairy cows. To identify an optimal time for sampling, we collected buccal swab and rumen samples at six different time points relative to animal feeding. We then evaluated several biases in these samples using a machine learning classifier (random forest) to select taxa that discriminate between buccal swab and rumen samples. Differences in the inverse Simpson's diversity, Shannon's evenness, and Bray-Curtis dissimilarities between methods were significantly less apparent when sampling was performed prior to morning feeding ( < 0.05), suggesting that this time point was optimal for representative sampling. In addition, the random forest classifier was able to accurately identify nonrumen taxa, including 10 oral and putative feed-associated taxa. Two highly prevalent (>60%) taxa in buccal and rumen samples had significant variance in relative abundances between sampling methods but could be qualitatively assessed via regular buccal swab sampling. This work not only provides new insights into the oral community of ruminants but also further validates and refines buccal swabbing as a method to assess the rumen bacterial in large herds. The gastrointestinal tracts of ruminants harbor a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health, and performance. While the influence of environmental factors on rumen microbes is well documented, the process by which host genetics influences the establishment and colonization of the rumen microbiota still needs to be elucidated. This knowledge gap is due largely to our inability to easily sample the rumen microbiota. There are three common methods for rumen sampling but all of them present at least one disadvantage, including animal welfare, sample quality, labor, and scalability. The development and validation of noninvasive methods, such as buccal swabbing, for large-scale rumen sampling is needed to support studies that require large sample sizes to generate reliable results. The validation of buccal swabbing will also support the development of molecular tools for the early diagnosis of metabolic disorders associated with microbial changes in large herds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.00861-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7440797PMC
August 2020

Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents.

Physiol Genomics 2020 08 22;52(8):333-346. Epub 2020 Jun 22.

Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin.

Development of a properly functioning gastrointestinal tract (GIT) at an early age is critical for the wellbeing and lifetime productivity of dairy cattle. The role of early microbial colonization on GIT development in neonatal cattle and the associated molecular changes remain largely unknown, particularly for the small intestine. In this study, we performed artificial dosing of exogenous rumen fluid during the early life of the calf, starting at birth through the weaning transition at 8 wk. Six calves were included in this study. At 8 wk of age, tissue from the ileum was collected and subjected to host transcriptome and microbial metatranscriptome analysis using RNA sequencing. A total of 333 genes showed significant differential expression (DE) (fold-change ≥2; adjusted < 0.1, mean read-count ≥10) between the treated and control calves. Gene ontology analysis indicated that these DE genes are predominantly associated with processes related to the host immune response ( < 0.0001). Association analysis between the host gene expression and the microbial genus abundance identified 57 genes as having significant correlation with the ileum microbial genera ( < 0.0001). Of these, three genes showed significant association with six microbial genera: lysozyme 2 (), fatty acid binding protein 5 (), and fucosyltransferase ). Specifically, the profound increase in expression of in treated calves suggests the initiation of antibacterial activity and innate response from the host. Despite the limitation of a relatively small sample size, this study sheds light on the potential impact of early introduction of microbes on the small intestine of calves.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1152/physiolgenomics.00005.2020DOI Listing
August 2020

Fecal microbiota transplantation for patients on antibiotic treatment with infection history (GRAFT): Study protocol for a phase II, randomized, double-blind, placebo-controlled trial to prevent recurrent infections.

Contemp Clin Trials Commun 2020 Jun 19;18:100576. Epub 2020 May 19.

Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.

Recurrent infections (rCDIs) are a burdensome problem. Patients with a history of CDI that are prescribed antibiotics are at a high risk for recurrence. Fecal microbiota transplantation (FMT) has been shown to be an effective treatment for rCDI, though there is little information on the impact of FMT with antibiotics on the gut microbiome. We are conducting a clinical trial of FMT to prevent rCDI in patients with a history of CDI currently taking antibiotics. Our primary objective is to determine the effect of FMT on the gut microbiome during antibiotic exposure. Our secondary aim is to assess safety and feasibility of using FMT as a prophylaxis for CDI. We plan to enroll 30 patients into a phase II randomized, double-blind, placebo-controlled trial with three arms: (1) 5 FMT capsules per day during antibiotic treatment and for 7 days post antibiotic cessation, (2) a one-time dose of 30 FMT capsules 48-72 h post cessation of antibiotic treatment, or (3) 5 placebo capsules per day during antibiotic treatment and for 7 days post antibiotic treatment. Patients provide stool samples throughout the duration of the study and are cultured Sequencing of the V4 region of the 16S rRNA gene will be carried out to assess the gut microbiota. Results of this study will provide information on the impact of FMT on the gut microbiome as well as the necessary data to examine whether or not prophylactic FMT should be explored further as a way to prevent CDI recurrence.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.conctc.2020.100576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7270544PMC
June 2020

Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity.

FEMS Microbiol Ecol 2020 06;96(6)

Department of Biology, Williams College, Science Center South Building Room 222, Williamstown, MA, USA 01267.

Artificial sweeteners have been shown to induce glucose intolerance by altering the gut microbiota; however, little is known about the effect of stevia. Here, we investigate whether stevia supplementation induces glucose intolerance by altering the gut microbiota in mice, hypothesizing that stevia would correct high fat diet-induced glucose intolerance and alter the gut microbiota. Mice were split into four treatment groups: low fat, high fat, high fat + saccharin and high fat + stevia. After 10 weeks of treatment, mice consuming a high fat diet (60% kcal from fat) developed glucose intolerance and gained more weight than mice consuming a low fat diet. Stevia supplementation did not impact body weight or glucose intolerance. Differences in species richness and relative abundances of several phyla were observed in low fat groups compared to high fat, stevia and saccharin. We identified two operational taxonomic groups that contributed to differences in beta-diversity between the stevia and saccharin groups: Lactococcus and Akkermansia in females and Lactococcus in males. Our results demonstrate that stevia does not rescue high fat diet-induced changes in glucose tolerance or the microbiota, and that stevia results in similar alterations to the gut microbiota as saccharin when administered in concordance with a high fat diet.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/femsec/fiaa079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233940PMC
June 2020

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota.

Front Cell Infect Microbiol 2020 28;10:73. Epub 2020 Feb 28.

Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.

The human gut microbiome has a great deal of interpersonal variation due to both endogenous and exogenous factors, like household pet exposure. To examine the relationship between having a pet in the home and the composition and diversity of the adult gut microbiome, we conducted a case-control study nested in a larger, statewide study, the Survey of the Health of Wisconsin. Stool samples were collected from 332 participants from unique households and analyzed using 16S rRNA sequencing on the Illumina MiSeq. One hundred and seventy-eight participants had some type of pet in the home with dogs and cats being the most prevalent. We observed no difference in alpha and beta diversity between those with and without pets, though seven OTUs were significantly more abundant in those without pets compared to those with pets, and four were significantly more abundant in those with pets. When stratifying by age, seven of these remained significant. These results suggest that pet ownership is associated with differences in the human gut microbiota. Further research is needed to better characterize the effect of pet ownership on the human gut microbiome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcimb.2020.00073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7058978PMC
March 2021

Toxic tall fescue grazing increases susceptibility of the Angus steer fecal microbiota and plasma/urine metabolome to environmental effects.

Sci Rep 2020 02 12;10(1):2497. Epub 2020 Feb 12.

Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, USA.

Impaired thermoregulation and lowered average daily gains (ADG) result when livestock graze toxic endophyte (Epichloë coenophialum)-infected tall fescue (E+) and are hallmark signs of fescue toxicosis (FT), a disease exacerbated by increased temperature and humidity (+temperature-humidity index; +THI). We previously reported FT is associated with metabolic and microbiota perturbations under thermoneutral conditions; here, we assessed the influence of E+ grazing and +THI on the microbiota:metabolome interactions. Using high-resolution metabolomics and 16S rRNA gene sequencing, plasma/urine metabolomes and the fecal microbiota of Angus steers grazing non-toxic or E+ tall fescue were evaluated in the context of +THI. E+ grazing affected the fecal microbiota profile; +THI conditions modulated the microbiota only in E+ steers. E+ also perturbed many metabolic pathways, namely amino acid and inflammation-related metabolism; +THI affected these pathways only in E+ steers. Integrative analyses revealed the E+ microbiota correlated and co-varied with the metabolomes in a THI-dependent manner. Operational taxonomic units in the families Peptococcaceae, Clostridiaceae, and Ruminococcaceae correlated with production parameters (e.g., ADG) and with multiple plasma/urine metabolic features, providing putative FT biomarkers and/or targets for the development of FT therapeutics. Overall, this study suggests that E+ grazing increases Angus steer susceptibility to +THI, and offers possible targets for FT interventions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-59104-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016188PMC
February 2020

Characterization of microbial communities in ethanol biorefineries.

J Ind Microbiol Biotechnol 2020 Feb 17;47(2):183-195. Epub 2019 Dec 17.

Department of Food Science, University of Wisconsin, Madison, WI, USA.

Bacterial contamination of corn-based ethanol biorefineries can reduce their efficiency and hence increase their carbon footprint. To enhance our understanding of these bacterial contaminants, we temporally sampled four biorefineries in the Midwestern USA that suffered from chronic contamination and characterized their microbiomes using both 16S rRNA sequencing and shotgun metagenomics. These microbiotas were determined to be relatively simple, with 13 operational taxonomic units (OTUs) accounting for 90% of the bacterial population. They were dominated by Firmicutes (89%), with Lactobacillus comprising 80% of the OTUs from this phylum. Shotgun metagenomics confirmed our 16S rRNA data and allowed us to characterize bacterial succession at the species level, with the results of this analysis being that Lb. helveticus was the dominant contaminant in this fermentation. Taken together, these results provide insights into the microbiome of ethanol biorefineries and identifies a species likely to be commonly responsible for chronic contamination of these facilities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10295-019-02254-7DOI Listing
February 2020

Urinary lead concentration and composition of the adult gut microbiota in a cross-sectional population-based sample.

Environ Int 2019 12 10;133(Pt A):105122. Epub 2019 Sep 10.

Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin - Madison, 610 Walnut St, WARF 707, Madison, WI 53726, USA. Electronic address:

Background: Lead (Pb) is a ubiquitous environmental contaminant with an array of detrimental health effects in children and adults, including neurological and immune dysfunction. Emerging evidence suggests that Pb exposure may alter the composition of the gut microbiota, however few studies have examined this association in human populations. The purpose of this study was to examine the association between urinary Pb concentration and the composition of the adult gut microbiota in a population-based sample of adults.

Methods: Data used in this study were collected as part of the Survey of the Health of Wisconsin (SHOW) and its ancillary microbiome study. The SHOW is a household-based health examination survey of Wisconsin residents, collecting a variety of survey data on health determinants and outcomes, as well as objective measurements of body habitus, and biological specimens including urine. The ancillary microbiome study added additional questions and biological specimen collection, including stool, from participants age 18+. Pb concentration was analyzed in urine samples, and gut microbiota composition was assessed using DNA sequencing of the 16S rRNA V4 region, extracted from stool samples. Data processing and statistical analyses were performed in mothur, Python, R, and SAS.

Results: Of 696 participants, urinary Pb concentration was highest in those age 70+, females, those with a high school diploma or lower, current and former smokers, and those without indoor pets. In adjusted models, increasing urinary Pb levels were associated with increases in microbial α-diversity (p = 0.071) and richness (p = 0.005). Differences in microbial β-diversity were significantly associated (p = 0.003) with differences in urinary Pb level. Presence of Proteobacteria, including members of the Burkholderiales, was significantly associated with increased urinary Pb.

Conclusion: These results suggest that Pb exposure is associated with differences in the composition of the adult gut microbiota in a population-based human sample. Further investigation of this association is warranted.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.envint.2019.105122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7230144PMC
December 2019

The ruminal bacterial community in lactating dairy cows has limited variation on a day-to-day basis.

J Anim Sci Biotechnol 2019 19;10:66. Epub 2019 Aug 19.

1Department of Bacteriology, University of Wisconsin-Madison, 5159 MSB, 1550 Linden Drive, Madison, WI 53706 USA.

Dairy cows rely on a complex ruminal microbiota to digest their host-indigestible feed. Our ability to characterize this microbiota has advanced significantly due to developments in next-generation sequencing. However, efforts to sample the rumen, which typically involves removing digesta directly from the rumen via a cannula, intubation, or rumenocentesis, is costly and labor intensive. As a result, the majority of studies characterizing the rumen microbiota are conducted on samples collected at a single time point. Currently, it is unknown whether there is significant day-to-day variation in the rumen microbiota, a factor that could strongly influence conclusion drawn from studies that sample at a single time point. To address this, we examined day-to-day changes in the ruminal microbiota of lactating dairy cows using next-generation sequencing to determine if single-day sampling is representative of sampling across 3 consecutive days. We sequenced single-day solid and liquid fractions of ruminal digesta collected over 3 consecutive days from 12 cannulated dairy cows during the early, middle, and late stages of a single lactation cycle using the V4 region of the bacterial 16S rRNA gene. We then generated 97% similarity operational taxonomic units (OTUs) from these sequences and showed that any of the individual samples from a given 3-day sampling period is equivalent to the mean OTUs determined from the combined 3-d data set. This finding was consistent for both solid and liquid fractions of the rumen, and we thus conclude that there is limited day-to-day variability in the rumen microbiota.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40104-019-0375-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6698983PMC
August 2019

Characterising the gut microbiome in veterans with Gulf War Illness: a protocol for a longitudinal, prospective cohort study.

BMJ Open 2019 08 19;9(8):e031114. Epub 2019 Aug 19.

Research, William S Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA.

Introduction: Approximately 25%-35% of the 1991 Gulf War Veteran population report symptoms consistent with Gulf War Illness (GWI), a chronic, multi-symptom illness characterised by fatigue, pain, irritable bowel syndrome and problems with cognitive function. GWI is a disabling problem for Gulf War Veterans, and there remains a critical need to identify innovative, novel therapies.Gut microbiota perturbation plays a key role in the symptomatology of other chronic multi-symptom illnesses, including myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Given similarities between ME/CFS and GWI and the presence of gastrointestinal disorders in GWI patients, Veterans with GWI may also have gut abnormalities like those seen with ME/CFS. In this longitudinal cohort study, we are comparing the diversity (structure) and the metagenomes (function) of the gut microbiome between Gulf War Veterans with and without GWI. If we find differences in Veterans with GWI, the microbiome could be a target for therapeutic intervention to alleviate GWI symptoms.

Methods And Analysis: Participants answer questions about diet, exercise and lifestyle factors. Participants also complete a questionnaire (based on the Kansas case definition of GWI) regarding their medical history and symptoms; we use this questionnaire to group participants into GWI versus healthy control cohorts. We plan to enrol 52 deployed Gulf War Veterans: 26 with GWI and 26 healthy controls. Participants provide stool and saliva samples weekly for an 8-week period for microbiome analyses. Participants also provide blood samples at the beginning and end of this period, which we will use to compare measures of inflammation markers between the groups.

Ethics And Dissemination: The protocol was approved by the University of Wisconsin-Madison Health Sciences Institutional Review Board and the William S. Middleton Memorial Veterans Hospital Research and Development Committee. Results of this study will be submitted for publication in a peer-reviewed journal.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/bmjopen-2019-031114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707676PMC
August 2019

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

Genome Biol 2019 08 2;20(1):153. Epub 2019 Aug 2.

USDA-ARS U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-019-1760-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6676630PMC
August 2019

The Bacterial and Fungal Microbiota of Nelore Steers Is Dynamic Across the Gastrointestinal Tract and Its Fecal-Associated Microbiota Is Correlated to Feed Efficiency.

Front Microbiol 2019 25;10:1263. Epub 2019 Jun 25.

Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Brazil.

The ruminant gastrointestinal tract (GIT) microbiome plays a major role in the health, physiology and production traits of the host. In this work, we characterized the bacterial and fungal microbiota of the rumen, small intestine (SI), cecum and feces of 27 Nelore steers using next-generation sequencing and evaluated biochemical parameters within the GIT segments. We found that only the bacterial microbiota clustered according to each GIT segment. Bacterial diversity and richness as well as volatile fatty acid concentration was lowest in the SI. Taxonomic grouping of bacterial operational taxonomic units (OTUs) revealed that (24.61 ± SD 6.58%) and (20.87 ± SD 4.22%) were the two most abundant taxa across the GIT. For the fungi, the family dominated in all GIT segments, with the genus being the most abundant. Twenty-eight bacterial and six fungal OTUs were shared across all GIT segments in at least 50% of the steers. We also evaluated if the fecal-associated microbiota of steers showing negative and positive residual feed intake (n-RFI and p-RFI, respectively) was associated with their feed efficiency phenotype. Diversity indices for both bacterial and fungal fecal microbiota did not vary between the two feed efficiency groups. Differences in the fecal bacterial composition between high and low feed efficiency steers were primarily assigned to OTUs belonging to the families and and to the genus . The fungal OTUs shared across the GIT did not vary between feed efficiency groups, but 7 and 3 OTUs were found only in steers with positive and negative RFI, respectively. These results provide further insights into the composition of the Nelore GIT microbiota, which could have implications for improving animal health and productivity. Our findings also reveal differences in fecal-associated bacterial OTUs between steers from different feed efficiency groups, suggesting that fecal sampling may represent a non-invasive strategy to link the bovine microbiota with productivity phenotypes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2019.01263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6603086PMC
June 2019

Author Correction: Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow.

Sci Rep 2019 May 28;9(1):8116. Epub 2019 May 28.

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-44428-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6536682PMC
May 2019

Response of Beef Cattle Fecal Microbiota to Grazing on Toxic Tall Fescue.

Appl Environ Microbiol 2019 08 18;85(15). Epub 2019 Jul 18.

Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, USA

Tall fescue, the predominant southeastern United States cool-season forage grass, frequently becomes infected with an ergot alkaloid-producing toxic endophyte, Consumption of endophyte-infected fescue results in fescue toxicosis (FT), a condition that lowers beef cow productivity. Limited data on the influence of ergot alkaloids on rumen fermentation profiles or ruminal bacteria that could degrade the ergot alkaloids are available, but how FT influences the grazing bovine fecal microbiota or what role fecal microbiota might play in FT etiology and associated production losses has yet to be investigated. Here, we used 16S rRNA gene sequencing of fecal samples from weaned Angus steers grazing toxic endophyte-infected (E+;  = 6) or nontoxic (Max-Q;  = 6) tall fescue before and 1, 2, 14, and 28 days after pasture assignment. Bacteria in the and phyla comprised 90% of the Max-Q and E+ steer fecal microbiota throughout the trial. Early decreases in the family and delayed increases of the and families were among the major effects of E+ grazing. E+ also increased abundances within the , , and phyla and the family. Multiple operational taxonomic units classified as and were correlated negatively with weight gains (lower in E+) and positively with respiration rates (increased by E+). These data provide insights into how E+ grazing alters the Angus steer microbiota and the relationship of fecal microbiota dynamics with FT. Consumption of E+ tall fescue has an estimated annual $1 billion negative impact on the U.S. beef industry, with one driver of these costs being lowered weight gains. As global agricultural demand continues to grow, mitigating production losses resulting from grazing the predominant southeastern United States forage grass is of great value. Our investigation of the effects of E+ grazing on the fecal microbiota furthers our understanding of bovine fescue toxicosis in a real-world grazing production setting and provides a starting point for identifying easy-to-access fecal bacteria that could serve as potential biomarkers of animal productivity and/or FT severity for tall fescue-grazing livestock.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.00032-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643230PMC
August 2019

Laryngotracheal Microbiota in Adult Laryngotracheal Stenosis.

mSphere 2019 05 1;4(3). Epub 2019 May 1.

Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, USA

Laryngotracheal stenosis is an obstructive respiratory disease that leads to voicing difficulties and dyspnea with potential life-threatening consequences. The majority of incidences are due to iatrogenic etiology from endotracheal tube intubation; however, airway scarring also has idiopathic causes. While recent evidence suggests a microbial contribution to mucosal inflammation, the microbiota associated with different types of stenosis has not been characterized. High-throughput sequencing of the V4 region of the16S rRNA gene was performed to characterize the microbial communities of 61 swab samples from 17 iatrogenic and 10 adult idiopathic stenosis patients. Nonscar swabs from stenosis patients were internal controls, and eight swabs from four patients without stenosis represented external controls. Significant differences in diversity were observed between scar and nonscar samples and among sample sites, with decreased diversity detected in scar samples and the glottis region. Permutational analysis of variance (PERMANOVA) results revealed significant differences in community composition for scar versus nonscar samples, etiology type, sample site, groups (iatrogenic, idiopathic, and internal and external controls), and individual patients. Pairwise Spearman's correlation revealed a strong inverse correlation between and among all samples. Finally, bacteria in the family were found to be distinctly associated with idiopathic stenosis samples in comparison with external controls. Our findings suggest that specific microbiota and community shifts are present with laryngotracheal stenosis in adults, with members of the family , including the known pathogens and , identified in idiopathic scar. Further work is warranted to elucidate the contributing role of bacteria on the pathogenesis of laryngotracheal stenosis. The laryngotracheal region resides at the intersection between the heavily studied nasal cavity and lungs; however, examination of the microbiome in chronic inflammatory conditions of the subglottis and trachea remains scarce. To date, studies have focused on the microbiota of the vocal folds, or the glottis, for laryngeal carcinoma, as well as healthy larynges, benign vocal fold lesions, and larynges exposed to smoking and refluxate. In this study, we seek to examine the structure and composition of the microbial community in adult laryngotracheal stenosis of various etiologies. Due to the heterogeneity among the underlying pathogenesis mechanisms and clinical outcomes seen in laryngotracheal stenosis disease, we hypothesized that different microbial profiles will be detected among various stenosis etiology types. Understanding differences in the microbiota for subglottic stenosis subtypes may shed light upon etiology-specific biomarker identification and offer novel insights into management approaches for this debilitating disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphereDirect.00211-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6495342PMC
May 2019

Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs.

Environ Microbiol 2019 07 11;21(7):2333-2346. Epub 2019 Apr 11.

Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, 100081, Beijing, China.

Early gut microbial colonization is important for postnatal metabolic and immune development. However, little is known about the effects of different feeding modes (suckling versus bottle-feeding) or microbial sources on this process in farm animals. We found that suckled and bottle-fed newborn lambs had their own distinct gut microbiota. Results from 16S rRNA gene sequencing and qPCR showed that, compared with suckling, bottle feeding significantly increased the abundances of Escherichia/Shigella, Butyricicoccus, and Clostridium XlVa, while significantly decreased the abundance of Clostridium XI. The higher levels of Escherichia/Shigella in bottle-fed lambs suggest that artificial feeding may increase the number of potential pathogens and delay the establishment of the anaerobic environment and anaerobic microbes. Feeding modes also affected the direct transmission of bacteria from the mother and the environment to newborns. The SourceTracker analysis estimated that the early gut microbes of suckled lambs were mainly derived from the mother's teats (43%) and ambient air (28%); whereas those of bottle-fed lambs were dominated by bacteria from the mother's vagina (46%), ambient air (31%), and the sheep pen floor (12%). These findings advance our understanding of gut microbiota in early life and may help design techniques to improve gut microbiota and health.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.14614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6849743PMC
July 2019

Bacterial Communities in the Alpaca Gastrointestinal Tract Vary With Diet and Body Site.

Front Microbiol 2018 18;9:3334. Epub 2019 Jan 18.

Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States.

Gut -associated microbes ('gut microbiota') impact the nutrition of their hosts, especially in ruminants and pseudoruminants that consume high-cellulose diets. Examples include the pseudoruminant alpaca. To better understand how body site and diet influence the alpaca microbiota, we performed three 16S rRNA gene surveys. First, we surveyed the compartment 1 (C1), duodenum, jejunum, ileum, cecum, and large intestine (LI) of alpacas fed a grass hay (GH; tall fescue) or alfalfa hay (AH) diet for 30 days. Second, we performed a C1 survey of alpacas fed a series of 2-week mixed grass hay (MGH) diets supplemented with ∼25% dry weight barley, quinoa, amaranth, or soybean meal. Third, we examined the microbial differences of alpacas with normal versus poor body condition. Samples from GH- and AH-fed alpacas grouped by diet and body site but none of the four supplements significantly altered C1 microbiota composition, relative to each other, and none of the OTUs were differentially abundant between alpacas with normal versus poor body conditions. Taken together, the findings of a diet- and body-site specific alpaca microbiota are consistent with previous findings in ruminants and other mammals, but we provide no evidence to link changes in alpaca body condition with variation in microbiota relative abundance or identity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2018.03334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345687PMC
January 2019

Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow.

Sci Rep 2019 01 28;9(1):790. Epub 2019 Jan 28.

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.

In mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to directly interrogate the role of early gut/rumen microbial colonization on GIT development or host health in neonatal ruminants through artificial manipulation of the rumen microbiome. Thus, the molecular changes associated with bacterial colonization are largely unknown in cattle. In this study, we dosed young calves with exogenous rumen fluid obtained from an adult donor cow, starting at birth, and repeated every other week until six weeks of age. Eight Holstein bull calves were included in this study and were separated into two groups of four: the first group was treated with rumen content freshly extracted from an adult cow, and the second group was treated with sterilized rumen content. Using whole-transcriptome RNA-sequencing, we investigated the transcriptional changes in the host liver, which is a major metabolic organ and vital to the calf's growth performance. Additionally, the comparison of rumen epimural microbial communities between the treatment groups was performed using the rRNA reads generated by sequencing. Liver transcriptome changes were enriched with genes involved in cell signaling and protein phosphorylation. Specifically, up-regulation of SGPL1 suggests a potential increase in the metabolism of sphingolipids, an essential molecular signal for bacterial survival in digestive tracts. Notably, eight genera, belonging to four phyla, had significant increases in abundance in treated calves. Our study provides insight into host liver transcriptome changes associated with early colonization of the microbial communities in neonatal calves. Such knowledge provides a foundation for future probiotics-based research in microbial organism mediated rumen development and nutrition in ruminants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-37033-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349911PMC
January 2019
-->