scholarly journals Characterization of the microbiota associated with 12-week-old bovine fetuses exposed to divergent in utero nutrition

2021 ◽  
Author(s):  
Samat Amat ◽  
Devin B Holman ◽  
Kaycie Schmidt ◽  
Kacie L McCarthy ◽  
Sheri T Dorsam ◽  
...  
Keyword(s):  
Microbial Community ◽  
Allantoic Fluid ◽  
Shannon Index ◽  
Rrna Gene ◽  
Sample Type ◽  
Microscopy Imaging ◽  
Tissue Samples ◽  
Early Gestation ◽  
Bacterial Phyla ◽  
Bovine Fetuses

A recent study reported the existence of a diverse microbiota in 5-to-7-month-old calf fetuses, suggesting that colonization of the bovine gut with so-called 'pioneer' microbiota may begin during mid-gestation. In the present study, we investigated 1) the presence of microbiota in bovine fetuses at early gestation (12 weeks), and 2) whether the fetal microbiota is influenced by the maternal rate of gain or dietary supplementation with vitamins and minerals (VTM) during early gestation. Amniotic and allantoic fluids, and intestinal and placental (cotyledon) tissue samples obtained from fetuses (n = 33) on day 83 of gestation were processed for the assessment of fetal microbiota using 16S rRNA gene sequencing. The sequencing results revealed that a diverse and complex microbial community was present in each of these fetal compartments evaluated. Allantoic and amniotic fluids, and fetal intestinal and placenta microbiota each had distinctly different (0.047 ≥ R2 ≥ 0.019, P ≤ 0.031) microbial community structures. Allantoic fluid had a greater (P < 0.05) microbial richness (number of OTUs) (Mean 122) compared to amniotic fluid (84), intestine (63) and placenta (66). Microbial diversity (Shannon index) was similar for the intestinal and placental samples, and both were less diverse compared with fetal fluid microbiota (P < 0.05). Thirty-nine different archaeal and bacterial phyla were detected across all fetal samples, with Proteobacteria (55%), Firmicutes (16.2%), Acidobacteriota (13.6%) and Bacteroidota (5%) predominating. Among the 20 most relatively abundant bacterial genera, Acidovorax, Acinetobacter, Brucella, Corynebacterium, Enterococcus, Exiguobacterium and Stenotrophomonas differed by fetal sample type (P < 0.05). A total of 55 taxa were shared among the four different microbial communities. qPCR of bacteria in the intestine and placenta samples as well as scanning electron microscopy imaging of fetal fluids provided additional evidence for the presence of a microbiota in these samples. Minor effects of maternal rate of gain and VTM supplementation, and their interactions on microbial richness and composition were detected. Overall, the results of this study indicate that colonization with pioneer microbiota may occur during early gestation in bovine fetuses, and that that the maternal nutritional regime during gestation may influence the early fetal microbiota.

PSII-B-28 Investigation of the presence of bacterial microbiota in 12-week-old bovine fetuses

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 352-352
Author(s):  
Samat Amat ◽  
Devin B Holman ◽  
Kaycie Schmidt ◽  
kacie L L McCarthy ◽  
Sheri T T Dorsam ◽  
...  
Keyword(s):  
Microbial Community ◽  
Amniotic Fluid ◽  
Shannon Index ◽  
Rrna Gene ◽  
Sample Type ◽  
Microscopy Imaging ◽  
Tissue Samples ◽  
Early Gestation ◽  
Bacterial Phyla ◽  
Bovine Fetuses

Abstract A recent study reported the existence of a diverse microbiota in 5-to-7-month-old calf fetuses, suggesting that colonization of the bovine gut with so-called “pioneer” microbiota may begin during mid-gestation. In the present study, we investigated the microbiota in bovine fetuses at early gestation. Amniotic and allantoic fluids, and intestinal and placental (cotyledon) tissue samples harvested from fetuses (n = 33) on day 83 of gestation were processed for the assessment of fetal microbiota using 16S rRNA gene sequencing. The sequencing results revealed that a diverse and complex microbial community was present in allantoic and amniotic fluids, and fetal intestine and placenta on day 83 of gestation in beef cattle. Microbial community structure was significantly different between allantoic and amniotic fluid, and intestinal and placental microbiota (0.047 ≥ R2 ≥ 0.019, P ≤ 0.031). Allantoic fluid had a greater (P &lt; 0.05) microbial richness (number of OTUs) (122 ± 10) compared to amniotic fluid (84 ± 6), intestine (63 ± 7) and placenta (66 ± 6). Microbial diversity (Shannon index) was similar for the intestinal and placental samples, and both were less diverse compared to the fetal fluid microbiota (P &lt; 0.05). At the phylum level, 39 different archaeal and bacterial phyla were detected across all fetal samples, with Proteobacteria (55%), Firmicutes (16.2%), Actinobacteria (13.6%) and Bacteroidetes (5%) predominating. Among the 20 most relatively abundant bacterial genera, Acidovorax, Acinetobacter, Brucella, Corynebacterium, Enterococcus, Exiguobacterium and Stenotrophomonas differed by fetal sample type (P &lt; 0.05). A total of 55 taxa were shared among the four different microbial communities. qPCR of bacteria in the intestine and placenta samples as well as scanning electron microscopy imaging of fetal fluids provided additional evidence for the presence of a microbiota in these samples. Overall, the results of this study indicate that colonization with pioneer microbiota may occur during early gestation in bovine fetuses.

scholarly journals Succession of bacterial communities on carrion is independent of vertebrate scavengers

2019 ◽  
Author(s):  
Cody R. Dangerfield ◽  
Ethan Frehner ◽  
Evan Buechley ◽  
Çağan H. Şekercioğlu ◽  
William J. Brazelton
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Rrna Gene ◽  
Scavenging Activity ◽  
Ecological Interactions ◽  
Tissue Samples ◽  
Ultimate Result ◽  
Community Shifts ◽  
Micro Organisms ◽  
Carrion Decomposition

AbstractThe decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by scavenging.

scholarly journals Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Luis M. Rodriguez-R ◽  
Santosh Gunturu ◽  
James M. Tiedje ◽  
James R. Cole ◽  
Konstantinos T. Konstantinidis
Keyword(s):  
Microbial Community ◽  
Shannon Index ◽  
Sequence Diversity ◽  
Metagenomic Data ◽  
Reference Database ◽  
Rrna Gene ◽  
Data Sets ◽  
Data Set ◽  
Genomic Study ◽  
Culture Independent

ABSTRACT Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k -mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity ( N d ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that N d additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes. IMPORTANCE Estimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and limiting statistical approaches to quantify diversity. Here we described Nonpareil 3, a new bioinformatics algorithm that circumvents several of these limitations and thus can facilitate culture-independent studies in clinical or environmental settings, independent of the sequencing platform employed. In addition, we present a new metric of sequence diversity based on rarefied coverage and demonstrate its use in communities from diverse ecosystems.

scholarly journals The microbiome of the pelagic tunicate Dolioletta gegenbauri: a potential link between the grazing and microbial food web

2022 ◽  
Author(s):  
Tiago Pereira ◽  
Tina Walters ◽  
Hisham El-Shaffey ◽  
Holly Bik ◽  
Marc Frischer
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Rrna Gene ◽  
Natural Seawater ◽  
Sample Type ◽  
Fecal Pellets ◽  
Feeding Experiments ◽  
Gene Copies ◽  
Order Of Magnitude ◽  
Pelagic Tunicate

Doliolids often form massive blooms during upwelling conditions in sub-tropical shelves. However, their trophic role, including their nutritious fecal pellets, in pelagic marine food webs remains poorly investigated. In this study, we performed three independent feeding experiments of cultured Dolioletta gegenbauri and used qPCR analysis and 16S rRNA metabarcoding to characterize the microbial community associated with full gut (FG) and empty (EG) doliolids, fresh (FP2Hrs) and senescing (FP24Hrs) fecal pellets, and the surrounding natural seawater (SW). Bacterial abundance (i.e., 16S rRNA gene copies) in EG samples was an order of magnitude lower than in SW and three orders lower than in FP24Hrs. Diversity analyses, based on the 16S rRNA metabarcoding data, supported a richer microbial community in SW, FP2Hrs, FP24Hrs, and FG samples. Furthermore, microbial community structure was determined by sample type, with FG samples appearing more similar to either FP2Hrs or FP24Hrs. These patterns resulted from the higher number of shared ASVs and consequently the contribution of similar major bacterial taxa (e.g., Rhodobacteraceae, Pirellulaceae). These observations support the hypothesis that there are significant ecological and trophic interactions between D. gegenbauri and the ocean microbiome. Predicted gene function recovered many genes related to key processes in the marine environment and supported greater similarity between FP2Hrs, FP24Hrs, and FG samples. These observations suggest that pelagic marine bacteria are utilized by D. gegenbauri to digest captured prey particles, and the subsequent release of fecal pellets supports the rapid proliferation of distinct microbial communities which likely influence key biogeochemical processes in the ocean.

scholarly journals Variation in Microbial Community Profiles and Their Energy Metabolism Predictions Under the Influence of Pure and Mixed Fertilizer in Soil Microcosms

2021 ◽  
Author(s):  
Mohsin Gulzar Barq ◽  
Muhammad Mabashar Hassan ◽  
Nicola Lorenz ◽  
Noshaba Hassan Malik ◽  
Richard Dick ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Archaeal Community ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Community Shift ◽  
Environmental Perturbations ◽  
Metabolic Functions ◽  
Underlying Mechanisms ◽  
The Impact

Abstract The impact of environmental perturbations (e.g., nitrogen (N), phosphorus (P), potassium (K) and rice straw (Rs)) on the dynamics of soil bacterial and archaeal community are multifactor dependent and seeks more investigation concerning underlying mechanisms. Current study was designed to establish the effect of pure and mixed fertilizers on microbial community profiles in paddy soil. A short-term microcosm based experiment was established in which each microcosm is amended with N as C(H2N)2O, P and K as KH2PO4, K as KCl and Rs with concentrations equivalent to 160 kg N ha−1, 60 kg P ha−1, 130 kg K ha−1 and 1% respectively. Soil pH, electrical conductivity (EC), total C (TC), total nitrogen (TN), organic matter (OM), available K (AK) and extractable P (EP) were evaluated. To understand the microbial community variation in soil and to predict their metabolic functions, a high throughput sequencing (HTS) approach of 16S rRNA gene along with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was employed and analyzed. The results showed that microbial richness and diversity were increased under all amendments compared to control. Proteobacteria, Actinobacteria and Firmicutes were dominant bacterial phyla. In all amendments, regarding relative abundance, Chloroflexi, Bacteroidetes and Verrucomicrobia showed positive while Actinobacteria, Acidobacteria and Gemmatimonadetes showed negative trends when compared with controlled observations. Thaumarchaeota and Euryarchaeota were dominant archaeal phyla and exhibited increasing and decreasing trends, respectively. The PICRUSt indicated microbial community shift significantly towards amino acid, carbohydrate, energy, and lipid metabolism while less towards glycan biosynthesis, synthesis of secondary metabolites, terpenoids and biodegradation. Regarding metabolism (methane metabolism), most and least responsive treatments were predicted to be KP and controls, respectively. These findings enhanced our understanding regarding soil quality, fertilizer composition and their impact on microbial diversity.

Analysis of changes in the microbial community structure and physicochemical properties during the fermentation of sand crab juice

2021 ◽  
Author(s):  
Meiyan Luo ◽  
Leilei Chen ◽  
Huanming Liu ◽  
Jiahui Jiang ◽  
Chongxi Lai ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Isolation Technique ◽  
Bacterial Phyla ◽  
Staphylococcus Equorum ◽  
Rrna Gene Sequencing

Abstract The structure of the microbial community during sand crab juice fermentation was analyzed using culture-based methods and high-throughput 16S rRNA gene sequencing. Additionally, the changes in amino acid nitrogen (AAN) and total volatile basic nitrogen (TVB-N) were evaluated. Staphylococcus equorum, Staphylococcus arlettae, Staphylococcus saprophyticus, Salinicoccus amylolyticus, and Bacillus cereus were isolated by traditional culture isolation technique. The Good's coverage obtained by high-throughput sequencing was over 99.5%, and the Chao1 and Simpson indices showed small fluctuations, indicating that the species abundance and diversity did not change significantly during the fermentation process, although the abundance decreased. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant bacterial phyla observed during fermentation, whereas Aquabacterium, Roseovarius, Muribaculaceae, and Silicimonas were the dominant bacterial genera. The AAN content increased from 0.15 to 0.43 g/100 mL during the 15-day fermentation, indicating the production of small peptides and amino acids during fermentation. The TVB-N content (25.2 mg/100 mL) on day 15 indicated slight spoilage of sand crab juice, although the freshness conformed to the production standard. These results provide a theoretical basis for improving the quality and optimizing the production process of sand crab juice.

scholarly journals Effect of Chicken Manure-Based Fertiliser on Bacterial Communities and Diversity of Tomato Endosphere Microbiota

2021 ◽  
Vol 67 (3) ◽  
pp. 144-154
Author(s):  
Hafeez Ul Haq ◽  
Ye Li ◽  
Lingyue Jin ◽  
Ting Zhang ◽  
Linjie Cheng ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Chicken Manure ◽  
Rrna Gene ◽  
Beneficial Bacteria ◽  
Bacterial Phyla ◽  
Frequent Use ◽  
Significant Difference ◽  
Harmful Effects

Abstract The frequent use of chemical fertiliser produces harmful effects on the soil ecosystem. Therefore, biocompatible methods are used to improve plant health and production through natural fertiliser or plant beneficial microorganisms. This study aims to investigate the effect of amended chicken manure-based natural fertiliser on bacterial communities and plant beneficial bacteria of tomato endosphere microbiome using the high throughput 16S rRNA gene amplicon sequencing. The results showed Proteobacteria (89.4 ± 4.7% to 86.7 ± 3.9%), Actinobacteria (6.03 ± 2.9% to 3.56 ± 2.1%), and Firmicutes (3.34 ± 1.3% to 0.59 ± 0.3%) as the dominant bacterial phyla of tomato endophytic microbiome. Pseudomonas and Bacillus were the most abundant identifiable genera in the chicken manure root (CMR) (amended manure treatments) sample. There was no significant difference in alpha bacterial diversity (Shannon index: p = 0.48) and species richness (Chao 1: p = 0.43) between control original root (OR) and CMR. However, the distribution of the dominant phyla was mainly affected by manure fertilisation. The non-metric multidimensional scaling (NMDS) and PCoA of beta diversity analysis suggested a significant separation in bacterial communities of tomato endophytes between CMR and OR. The most differently abundant bacterial taxa belong to Bacteroidetes in the OR group, whereas the beneficial bacterial communities of Actinobacteria and Firmicutes were more abundant in the CMR group. Therefore, the chicken manure application can significantly affect bacterial communities of tomatoes´ root endophytic microbiome and effectively improve the abundance of the beneficial microbes as biofertilisers.

scholarly journals Succession of bacterial communities on carrion is independent of vertebrate scavengers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9307 ◽  
Author(s):  
Cody R. Dangerfield ◽  
Ethan H. Frehner ◽  
Evan R. Buechley ◽  
Çağan H. Şekercioğlu ◽  
William J. Brazelton
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Rrna Gene ◽  
Scavenging Activity ◽  
Ecological Interactions ◽  
Tissue Samples ◽  
Ultimate Result ◽  
Community Shifts ◽  
Micro Organisms ◽  
Carrion Decomposition

The decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by vertebrate scavenging.

Composition of seagrass phyllosphere microbial communities suggests rapid environmental regulation of community structure

2021 ◽  
Author(s):  
Margaret A Vogel ◽  
Olivia U Mason ◽  
Thomas E Miller
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Host Plant ◽  
Environmental Conditions ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Community Members ◽  
Bacterial Phyla ◽  
Primary Driver ◽  
Rrna Gene Sequencing

Abstract Recent studies have revealed that seagrass blade surfaces, also known as the phyllosphere, are rich habitats for microbes; however, the primary drivers of composition and structure in these microbial communities are largely unknown. This study utilized a reciprocal transplant approach between two sites with different environmental conditions combined with 16S rRNA gene sequencing (iTag) to examine the relative influence of environmental conditions and host plant on phyllosphere community composition of the seagrass Thalassia testudinum. After thirty days, identity of phyllosphere microbial community members was more similar within the transplant sites than between despite differences in the source of host plant. Additionally, the diversity and evenness of these communities was significantly different between the two sites. These results indicated that local environmental conditions can be a primary driver in structuring seagrass phyllosphere microbial communities over relatively short time scales. Composition of microbial community members in this study also deviated from those in previous seagrass phyllosphere studies with a higher representation of candidate bacterial phyla and archaea than previously observed. The capacity for seagrass phyllosphere microbial communities to shift dramatically with environmental conditions, including ecosystem perturbations, could significantly affect seagrass-microbe interactions in ways that may influence the health of the seagrass host.

scholarly journals Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert C. Kaplan ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
Martha L. Daviglus ◽  
...  
Keyword(s):  
Community Health ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Health Study ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Hispanic Community ◽  
The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

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