The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot

Abstract Feed is the greatest cost of animal production, so reducing it is critical to increase producer profits. In ruminants, the microbial population within the gastrointestinal tract (GIT) is critical to nutrient digestion and absorption in both the rumen and the hindgut. The objective of this study was to determine the bacterial taxonomic profile of the rumen, cecum, and feces of feedlot steers at slaughter in order to link feed efficiency and the GIT bacterial populations from these three locations. Twenty commercial Angus steers were selected and divided into two groups according to their residual feed intake (RFI) classification determined during the feedlot-finishing period: high-RFI (n = 10) and low-RFI (n = 10). After the ruminal, cecal, and fecal samples were collected at slaughter, DNA extraction and 16S rRNA gene sequencing were performed on them to determine their bacterial composition. One-way ANOVA was performed on the animal performance data, alpha diversities, and bacterial abundances using RFI classification as the fixed effect. Overall, the ruminal bacterial population was the most different in terms of taxonomic profile compared with the cecal and fecal populations as revealed by beta diversity analysis (P < 0.001). Moreover, bacterial richness (Chao1) was greatest (P = 0.01) in the rumen of the high-RFI group compared with the low-RFI group. In contrast, bacterial richness and diversity in the intestinal environment showed that Chao1 was greater (P = 0.01) in the cecum, and the Shannon diversity index was greater in both the cecum and feces of low-RFI compared with high-RFI steers (P = 0.01 and P < 0.001, respectively). Ruminococcaceae was more abundant in the low-RFI group in the cecum and feces (P = 0.01); fecal Bifidobacteriaceae was more abundant in high-RFI steers (P = 0.03). No correlations (P ≥ 0.13) between any ruminal bacterial family and RFI were detected; however, Ruminococcaceae, Mogibacteriaceae, Christensenellaceae, and BS11 were negatively correlated with RFI (P < 0.05) in the cecum and feces. Succinivibrionaceae in the cecum was positively correlated with RFI (P = 0.05), and fecal Bifidobacteriaceae was positively correlated with RFI (P = 0.03). Results collectively indicate that in addition to the ruminal bacteria, the lower gut bacterial population has a significant impact on feed efficiency and nutrient utilization in feedlot steers; therefore, the intestinal bacteria should also be considered when examining the basis of ruminant feed efficiency.

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The Impact of Pre-Slaughter Fasting on the Ruminal Microbial Population of Commercial Angus Steers

Microorganisms ◽

10.3390/microorganisms9122625 ◽

2021 ◽

Vol 9 (12) ◽

pp. 2625

Author(s):

Christina Breanne Welch ◽

Jeferson M. Lourenco ◽

Darren S. Seidel ◽

Taylor Rae Krause ◽

Michael J. Rothrock ◽

...

Keyword(s):

Diversity Index ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Ecosystem Structure ◽

Opportunistic Pathogens ◽

Slaughter Cattle ◽

Before And After ◽

Ruminal Microbiota ◽

Rrna Gene Sequencing ◽

The Impact

Diet impacts the composition of the ruminal microbiota; however, prior to slaughter, cattle are fasted, which may change the ruminal microbial ecosystem structure and lead to dysbiosis. The objective of this study was to determine changes occurring in the rumen after pre-slaughter fasting, which can allow harmful pathogens an opportunity to establish in the rumen. Ruminal samples were collected before and after pre-slaughter fasting from seventeen commercial Angus steers. DNA extraction and 16S rRNA gene sequencing were performed to determine the ruminal microbiota, as well as volatile fatty acid (VFA) concentrations. Microbial richness (Chao 1 index), evenness, and Shannon diversity index all increased after fasting (p ≤ 0.040). During fasting, the two predominant families Prevotellaceae and Ruminococcaceae decreased (p ≤ 0.029), whereas the remaining minor families increased (p < 0.001). Fasting increased Blautia and Methanosphaera (p ≤ 0.003), while Campylobacter and Treponema tended to increase (p ≤ 0.086). Butyrate concentration tended to decrease (p = 0.068) after fasting. The present findings support that fasting causes ruminal nutrient depletion resulting in dysbiosis, allowing opportunistic pathogens to exploit the void in the ruminal ecological niche.

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Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting

The International Journal of Neuropsychopharmacology ◽

10.1093/ijnp/pyaa070 ◽

2020 ◽

Author(s):

Yoshihiro Tomizawa ◽

Shunya Kurokawa ◽

Daiki Ishii ◽

Katsuma Miyaho ◽

Chiharu Ishii ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Diversity ◽

Depressive Disorders ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Shannon Index ◽

Rrna Gene ◽

Depression And Anxiety ◽

The Impact ◽

Whole Tree

Abstract Background The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication. Method We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions. Results We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P < .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively). Conclusion Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.

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In Vitro Fecal Fermentation Patterns of Arabinoxylan from Rice Bran on Gut Microbiota in Normal Weight and Overweight/Obese Subjects

Current Developments in Nutrition ◽

10.1093/cdn/nzaa062_017 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 1560-1560

Author(s):

Inah Gu ◽

Wing Shun Lam ◽

Daya Marasini ◽

Cindi Brownmiller ◽

Brett Savary ◽

...

Keyword(s):

Gut Microbiota ◽

Rice Bran ◽

Block Design ◽

16S Rrna Gene Sequencing ◽

Short Chain Fatty Acids ◽

Normal Weight ◽

Rrna Gene ◽

Gut Health ◽

The Impact

Abstract Objectives Arabinoxylan is a non-starch polysaccharide and rich in wheat, rice and many other cereal grains. Diets high in fiber help promoting gut health in obesity. The objective of this study was to investigate the impact of arabinoxylan from rice bran on the gut microbiota and short chain fatty acids (SCFA) in normal weight (NW) and overweight/obese (OO) subjects through in vitro fecal fermentation. Methods Arabinoxylan was extracted from rice bran fiber. For in vitro fecal fermentation, each fecal sample from NW (n = 6, 3 males and 3 females) and OO (n = 7, 3 males and 4 females) was diluted into anaerobic medium with three treatments: control (no substrates), fructooligosaccharides (FOS, a well-known prebiotic), and arabinoxylan. Samples were incubated at 37˚C and aliquots were taken at 0, 4, 8, 12 and 24 h. SCFA content from samples at all timepoints was analyzed using HPLC. Samples at 0 and 24 h were used for gut microbiota analysis through 16S rRNA gene sequencing. Statistical analyses were performed for the randomized complete block design, where the weight classes are confounded with blocks (subjects). Friedman test was used to determine the difference at 5% level of significance. Results As a result, arabinoxylan treatment significantly increased total SCFA concentration in both NW and OO subjects than control (P < 0.05), comparable to FOS treatment. Between weight classes under arabinoxylan treatment, OO group showed a significantly higher total SCFA content than NW group (P < 0.05). Arabinoxylan changed gut microbial population at the genus level, stimulating Bifidobacterium, Collinsella and Blautia and decreasing Clostridium XIVa and b, Dorea and Oscillibacter (P < 0.05). In addition, different microbiome population was shown in weight classes with three treatments, showing higher Bacteroides in NW and higher Prevotella in OO. Conclusions These results showed that arabinoxylan from rice bran modified gut microbiota in both weight classes, increasing total SCFA content. This study suggests that arabinoxylan from rice bran may have a potential impact on microbial gut health in obesity with prebiotic activities. Funding Sources University of Arkansas.

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Inbreeding Alters the Gut Microbiota of the Banna Minipig

Animals ◽

10.3390/ani10112125 ◽

2020 ◽

Vol 10 (11) ◽

pp. 2125

Author(s):

Limin Wei ◽

Bo Zeng ◽

Siyuan Zhang ◽

Feng Li ◽

Fanli Kong ◽

...

Keyword(s):

Gut Microbiota ◽

Gene Sequencing ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Rrna Gene Sequencing ◽

Isoleucine Metabolism ◽

Dominant Bacteria ◽

The Impact ◽

Predicted Function

The gut microbiota coevolve with the host and can be stably transmitted to the offspring. Host genetics plays a crucial role in the composition and abundance of gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity and the heterozygosity. In this study, we used 16S rRNA gene sequencing to compare the differences of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to understand the impact of inbreeding on the gut microbiota. Three dominant bacteria (Stenotrophlomonas, Streptococcus, and Lactobacillus) were steadily enriched in both the Diannan small-ear pig and Banna minipig inbred. After inbreeding, the gut microbiota alpha diversity and some potential probiotics (Bifidobacterium, Tricibacter, Ruminocaccae, Christensenellaceae, etc.) were significantly decreased, while the pathogenic Klebsiella bacteria was significantly increased. In addition, the predicted metagenomic analysis (PICRUSt2) indicated that several amino acid metabolisms (‘‘Valine, leucine, and isoleucine metabolism’’, ‘‘Phenylalanine, tyrosine, and tryptophan biosynthesis’’, ‘‘Histidine metabolism’’) were also markedly decreased after the inbreeding. Altogether our data reveal that host inbreeding altered the composition and the predicted function of the gut microbiome, which provides some data for the gut microbiota during inbreeding.

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Dichotomy between regulation of coral bacterial communities and calcification physiology under ocean acidification conditions

Applied and Environmental Microbiology ◽

10.1128/aem.02189-20 ◽

2021 ◽

Author(s):

A. Shore ◽

R. D. Day ◽

J. A. Stewart ◽

C.A. Burge

Keyword(s):

Ocean Acidification ◽

Bacterial Communities ◽

16S Rrna Gene Sequencing ◽

Ph Gradient ◽

Rrna Gene ◽

Seawater Ph ◽

Coral Health ◽

And Function ◽

The Impact

Ocean acidification (OA) threatens the growth and function of coral reef ecosystems. A key component to coral health is the microbiome, but little is known about the impact of OA on coral microbiomes. A submarine CO2 vent at Maug Island in the Northern Marianas Islands provides a natural pH gradient to investigate coral responses to long-term OA conditions. Three coral species (Pocillopora eydouxi, Porites lobata, and Porites rus) were sampled from three sites where mean seawater pH is 8.04, 7.98, and 7.94. We characterized coral bacterial communities (using 16S rRNA gene sequencing) and determined pH of the extracellular calcifying fluid (ECF) (using skeletal boron isotopes) across the seawater pH gradient. Bacterial communities of both Porites species stabilized (decreases in community dispersion) with decreased seawater pH, coupled with large increases in the abundance of Endozoicomonas, an endosymbiont. P. lobata experienced a significant decrease in ECF pH near the vent, whereas P. rus experienced a trending decrease in ECF pH near the vent. By contrast, Pocillopora exhibited bacterial community destabilization (increases in community dispersion), with significant decreases in Endozoicomonas abundance, while its ECF pH remained unchanged across the pH gradient. Our study shows that OA has multiple consequences on Endozoicomonas abundance and suggests that Endozoicomonas abundance may be an indicator of coral response to OA. We reveal an interesting dichotomy between two facets of coral physiology (regulation of bacterial communities and regulation of calcification), highlighting the importance of multidisciplinary approaches to understanding coral health and function in a changing ocean. IMPORTANCE Ocean acidification (OA) is a consequence of anthropogenic CO2 emissions that is negatively impacting marine ecosystems such as coral reefs. OA affects many aspects of coral physiology, including growth (i.e. calcification) and disrupting associated bacterial communities. Coral-associated bacteria are important for host health, but it remains unclear how coral-associated bacterial communities will respond to future OA conditions. We document changes in coral-associated bacterial communities and changes to calcification physiology with long-term exposure to decreases in seawater pH that are environmentally relevant under mid-range IPCC emission scenarios (0.1 pH units). We also find species-specific responses that may reflect different responses to long-term OA. In Pocillopora, calcification physiology was highly regulated despite changing seawater conditions. In Porites spp., changes in bacterial communities do not reflect a breakdown of coral-bacterial symbiosis. Insights into calcification and host-microbe interactions are critical to predicting the health and function of different coral taxa to future OA conditions.

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Biliary microbiota and bile acids composition in cholelithiasis

10.1101/469825 ◽

2018 ◽

Author(s):

Vyacheslav A. Petrov ◽

María A. Fernández-Peralbo ◽

Rico Derks ◽

Elena M. Knyazeva ◽

Nikolay V. Merzlikin ◽

...

Keyword(s):

Microbial Community ◽

Bile Acids ◽

Acid Concentration ◽

Gallstone Disease ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Taurocholic Acid ◽

Rrna Gene ◽

Microbial Composition ◽

Taxonomic Profile

AbstractBackgroundA functional interplay between BAs and microbial composition in gut is a well-documented phenomenon. In bile this phenomenon is far less studied and with this report we describe the interactions between the BAs and microbiota in this complex biological matrix.MethodologyThirty-seven gallstone disease patients of which twenty-one withOpisthorchis felineusinfection were enrolled in the study. The bile samples were obtained during laparoscopic cholecystectomy for gallstone disease operative treatment. Common bile acids composition were measured by LC-MS/MS using a column in reverse phase. For all patients gallbladder microbiota was previously analyzed with 16S rRNA gene sequencing on Illumina MiSeq platform. The associations between bile acids composition and microbiota were analysed.Principal findingsBile acids signature andO. felineusinfection status exerts influence on beta-diversity of bile microbial community. Direct correlations were found between taurocholic acid, taurochenodeoxycholic acid concentrations and alpha-diversity of bile microbiota. Taurocholic acid and taurochenodeoxycholic acid both shows positive associations with the presence of Chitinophagaceae family,MicrobacteriumandLutibacteriumgenera andPrevotella intermedia. Also direct associations were identified for taurocholic acid concentration and the presence of Actinomycetales and Bacteroidales orders,Lautropiagenus,Jeotgalicoccus psychrophilusandHaemophilus parainfluenzaeas well as for taurochenodeoxycholic acid and Acetobacteraceae family and Sphingomonas genus. There were no differences in bile acids concentrations between O.felineusinfected and non-infected patients.Conclusions/SignificanceAssociations between diversity, taxonomic profile of bile microbiota and bile acids levels were evidenced in patients with cholelithiasis. Increase of taurochenodeoxycholic acid and taurocholic acid concentration correlates with bile microbiota alpha-diversity and appearance of opportunistic pathogens. Alteration of bile acids signature could cause shifts in bile microbial community structure.

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Understanding host-microbiota interactions in the commercial piglet around weaning

Scientific Reports ◽

10.1038/s41598-021-02754-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Saladrigas-García ◽

M. D’Angelo ◽

H. L. Ko ◽

P. Nolis ◽

Y. Ramayo-Caldas ◽

...

Keyword(s):

Gene Expression ◽

Gut Microbiota ◽

Metabolic Response ◽

Negative Impact ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Swine Industry ◽

Weaning Stress ◽

Rrna Gene Sequencing ◽

The Impact

AbstractWeaning is a critical period in the life of pigs with repercussions on their health and welfare and on the economy of the swine industry. This study aimed to assess the effect of the commercial early weaning on gut microbiota, intestinal gene expression and serum metabolomic response via an integrated-omic approach combining 16S rRNA gene sequencing, the OpenArray gene expression technology and 1H-NMR spectroscopy. Fourteen piglets from different litters were sampled for blood, jejunum tissue and caecal content two days before (− 2d), and three days after (+ 3d) weaning. A clearly differential ordination of caecal microbiota was observed. Higher abundances of Roseburia, Ruminococcus, Coprococcus, Dorea and Lachnospira genera in weaned piglets compared to prior to weaning showed the quick microbial changes of the piglets’ gut microbiota. Downregulation of OCLN, CLDN4, MUC2, MUC13, SLC15A1 and SLC13A1 genes, also evidenced the negative impact of weaning on gut barrier and digestive functions. Metabolomic approach pinpointed significant decreases in choline, LDL, triglycerides, fatty acids, alanine and isoleucine and increases in 3-hydroxybutyrate after weaning. Moreover, the correlation between microbiota and metabolome datasets revealed the existence of metabolic clusters interrelated to different bacterial clusters. Our results demonstrate the impact of weaning stress on the piglet and give insights regarding the associations between gut microbiota and the animal gene activity and metabolic response.

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Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China

PeerJ ◽

10.7717/peerj.9500 ◽

2020 ◽

Vol 8 ◽

pp. e9500

Author(s):

Xiaojuan Chen ◽

Da He ◽

Lianfeng Zhou ◽

Yankun Cao ◽

Zhanjing Li

Keyword(s):

Algal Blooms ◽

Sequence Similarity ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Microbial Composition ◽

Jinsha River ◽

Kegg Pathways ◽

Significant Difference ◽

The Impact ◽

Hydropower Stations

Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks.

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The Gut Microbiome and Diabetes Status in the Multiethnic Cohort

Current Developments in Nutrition ◽

10.1093/cdn/nzaa061_078 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 1450-1450

Author(s):

Gertraud Maskarinec ◽

Phyllis Raquinio ◽

Bruce Kristal ◽

Lynne Wilkens ◽

Adrian Franke ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiome ◽

Diversity Index ◽

16S Rrna Gene Sequencing ◽

Sensu Stricto ◽

Rrna Gene ◽

Gram Negative ◽

Bonferroni Adjustment ◽

Multiethnic Cohort ◽

Diabetes Status

Abstract Objectives As features of the gut microbiome may promote the development of type 2 diabetes (T2D), we examined the hypothesis that gut microbiome composition differs by glycemic/diabetes status within a subset of the Multiethnic Cohort. We also estimated the association of lipopolysaccharide-binding protein (LBP) as a measure of circulating bacterial endotoxin with T2D. This outer membrane component of gram-negative bacteria may affect glucose metabolism. Methods In 2013–16, cohort members from 5 ethnic groups completed clinic visits, questionnaires, and stool collections. Participants with self-reported T2D and/or taking medication were considered T2D cases. Those with fasting glucose >125 and 100–125 mg/dL were classified as undiagnosed (UT2D) and prediabetes (PT2D). We characterized the gut microbiome through 16S rRNA gene sequencing (V1-V3). Plasma LBP was measured by ELISA. Linear regression was applied to estimate associations of gut microbiome community structure and LBP with T2D status adjusting for relevant confounders. Results Among 1756 participants (59.9–77.4 years), 315 (18%) were T2D, 158 (9%) UT2D, 518 (29%) PT2D, and 765 (44%) normoglycemic (NG). The Shannon diversity index was lower (6.30, 6.25, 6.28, 6.18; P = 0.02) and LBP was higher (26.0, 26.6, 28.6, 28.2 µg/mL; P = 0.0009) in T2D than NG participants. Of 10 phyla, Actinobacteria and Firmicutes were inversely associated with T2D status (P = 0.004). Six of 161 genera were significantly related to T2D status after Bonferroni adjustment: the abundance of Clostridium sensu stricto 1, Lachnospira, Lachnospiraceae NC2004, and Peptostreptococcaceae was lower, while Lachnospiraceae uncultured and Escherichia-Shigella were more abundant among T2D than NG participants. In general, those with PT2D and UT2D had values closer to NG than T2D individuals. Conclusions Participants with T2D showed a lower abundance of bacteria capable of fermenting plant polysaccharides and higher levels of gram-negative endotoxin-producing bacteria indicating that a less favorable pattern of gut microbiome community structure may contribute to T2D through endotoxin binding to toll-like receptors via LBP and activation of the NFkB pathway associated with chronic systemic inflammation. Funding Sources NIH grants P01CA169530, U01CA164973, P30CA071789, #UL1TR000130, R01HL140335.

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Investigation of Oral Microbiome in Donkeys and the Effect of Dental Care on Oral Microbial Composition

Animals ◽

10.3390/ani10122245 ◽

2020 ◽

Vol 10 (12) ◽

pp. 2245

Author(s):

Yiping Zhu ◽

Wuyan Jiang ◽

Reed Holyoak ◽

Bo Liu ◽

Jing Li

Keyword(s):

Dental Treatment ◽

16S Rrna Gene Sequencing ◽

Oral Microbiome ◽

Rrna Gene ◽

Microbial Composition ◽

Dental Procedures ◽

Significant Difference ◽

Dental Diseases ◽

Rrna Gene Sequencing ◽

The Impact

The objective of this study was to investigate the oral microbial composition of the donkey and whether basic dental treatment, such as dental floating, would make a difference to the oral microbial environment in donkeys with dental diseases using high-throughput bacterial 16S rRNA gene sequencing. Oral swab samples were collected from 14 donkeys with various dental abnormalities on day 0 (before treatment) and day 20 (twenty days after treatment). It is the first report focusing on the oral microbiome in donkeys with dental diseases and the impact of common dental procedures thereon. Identified in group Day 0 and group Day 20, respectively, were 60,439.6 and 58,579.1 operational taxonomic units (OTUs). Several taxa in Day 0 differed significantly from Day 20 at the phylum and genus levels, but no statistically significant difference was observed in richness and diversity of Day 0 and Day 20. The results also indicated that a larger-scale study focusing on healthy donkey oral microbiome, as well as the correlation of dental diseases and oral microbiomes at different time frames following more specific and consistent dental treatment, are warranted.

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