Characterization of Microbiome on Feces, Blood and Milk in Dairy Cows with Different Milk Leucocyte Pattern

Mastitis is an inflammatory disease of the mammary gland, caused by the invasion of microorganism on this site, associated with an altered immune response. Recent studies in this field hypothesize that the origin of these pathogens can also be from the gastrointestinal tract, through the entero-mammary pathway in relation to an increase in gut permeability. In this study, we wanted to investigate if inflammatory status of the mammary gland is related to an alteration of gut permeability. The microbiome of feces, blood and milk of lactating cows, recruited on the basis of the total somatic cell count and of the percentage of polymorphonuclear neutrophils and lymphocytes, was studied. Cows were divided into healthy (G), at risk of mastitis (Y) and with mastitis (R) classifications. The bacterial DNA was extracted and the V3 and V4 regions of 16S rRNA sequenced. Moreover, the quantification of total bacteria was performed with quantitative real-time PCR. A non-parametric Kruskal–Wallis test was applied at the phylum, family and genera levels and beta biodiversity was evaluated with the unweighted UniFrac distance metric. Significant differences between groups were found for the microbial composition of feces (Clostridiaceae, Turicibacteriaceae for family level and Clostridium, Dorea, SMB53 and Turicibacter for genus level), blood (Tenericutes for phylum level and Mycoplasma for genus level) and milk (OD1 and Proteobacteria for phylum level, Enterobacteriaceae and Moraxallaceae for family level and Olsenella and Rhodococcus for genus level). The beta biodiversity of feces and blood did not change between groups. Significant differences (p < 0.05) were observed between the beta diversity in milk of G group and Y group and between Y group and R group. The number of taxa in common between feces, blood and milk were 8 at a phylum, 19 at a family and 15 at a genus level. From these results, the bacterial crossing from gut to milk in cows was not confirmed but remained hypothetical and deserves further investigation.

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Microbiome Analysis Exploring Taxonomic Diversity in Kasaragod Dwarf and Holstein Crossbred Cattle

10.21203/rs.3.rs-1031096/v1 ◽

2021 ◽

Author(s):

Deepthi M ◽

Kumar Arvind ◽

Rituja Saxena ◽

Joby Pulikkan ◽

Vineet K Sharma ◽

...

Keyword(s):

High Throughput Sequencing ◽

Marker Gene ◽

Taxonomic Diversity ◽

Crossbred Cattle ◽

Microbial Composition ◽

Indigenous Cattle ◽

Animal Products ◽

Unifrac Distance ◽

Unweighted Unifrac ◽

Principle Coordinate Analysis

Abstract The indigenous cattle are efficient in converting low quality feeds and forage into animal products. Kasaragod Dwarf cattle, a unique non-descriptive native cattle of Kerala, India, are noted for their unique qualities, such as low feed intake, thermotolerance, greater resistance to diseases and A2 allelic variant milk. However, owing to the higher milk yield, Holstein crossbred cattle are given more importance over Kasaragod Dwarf. The hindgut microbiota plays a major role in various biological processes such as the digestion, vitamins synthesis, and immunity in cattle. In this study, we compared the hindgut microbiota of the Kasaragod Dwarf with the highly found, Holstein crossbred utilizing 16S rRNA high-throughput sequencing for a better understanding of the relationship between the host and microbial community. Four replicates of each 20 samples comprising two cattle type (n=10) were sequenced and analyzed. Marker gene-based taxonomic analysis affirmed variations in their microbial composition. Principle Coordinate Analysis (PCoA) using weighted and unweighted UniFrac distance matrices showed the distinct microbial architecture of the two cattle type. Random Forest analysis further confirmed the distinctness and revealed the signature taxa in K-Dwarf. The study observed the predominance of feed efficiency associated genera viz., Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Anaerostipes, Paludibacter, Elusimicrobium, Sutterella, Oribacterium, Coprobacillus, and Ruminobacter in Kasaragod Dwarf cattle. The study highlights the abundance of unique and beneficial hindgut microflora found in Kasaragod Dwarf, which may attest its importance over exotic cattle breeds viz., Holstein. To our knowledge, this is the first report of Kasaragod Dwarf cattle gut microbiome profiling. This study is pivotal towards developing genetic resources for the microbial population in K-Dwarf and how it could be differentiated from Holstein crossbred cattle.

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Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates

mSphere ◽

10.1128/msphere.00560-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 7

Author(s):

Francesco Multinu ◽

Sean C. Harrington ◽

Jun Chen ◽

Patricio R. Jeraldo ◽

Stephen Johnson ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Genomic Dna ◽

Rrna Gene ◽

Microbial Composition ◽

Unifrac Distance ◽

Β Diversity ◽

Unweighted Unifrac ◽

Stool Samples ◽

Community Representation

ABSTRACT Variability in representation of microbial communities can be caused by differences in microbial composition or artifacts introduced at sample collection or processing. Alterations in community representation introduced by variations in starting DNA concentrations have not been systematically investigated in stool samples. The goal of this study was to evaluate the effect of the genomic DNA (gDNA) concentration in the resulting 16S rRNA gene library composition and compare its effect to other sample processing variables in homogenized human fecal material. Compared to a gDNA input of 1 ng/μl, inputs of ≤1.6 × 10 −3 ng/μl resulted in a marked decrease in the concentration of the 16S rRNA gene amplicon ( P < 0.001). Low gDNA concentrations (≤1.6 × 10 −3 ng/μl) were also associated with a decrease ( P < 0.001) in the number of operational taxonomic units and significant divergence in β-diversity profiles (unweighted UniFrac distance, P < 0.001), as characterized by an overestimation of Proteobacteria and underestimation of Firmicutes . Even a gDNA concentration of 4 × 10 −2 ng/μl showed a significant impact on the β-diversity profile (unweighted UniFrac distance, P = 0.03). Overall, the gDNA concentration explained 22.4% to 38.1% of the microbiota variation based on various β-diversity measures ( P < 0.001). By comparison, the DNA extraction methods and PCR volumes tested did not significantly affect the microbial composition profile, and the PCR cycling method explained less than 3.7% of the microbiota variation (weighted UniFrac distance, P = 0.03). The 16S rRNA gene yield and the microbial community representation of human homogenized stool samples are significantly altered by gDNA template concentrations of ≤1.6 × 10 −3 ng/μl. In addition, data from studies with a gDNA input of ≤4 × 10 −2 ng/μl should be interpreted with caution. IMPORTANCE The genomic DNA input for stool samples utilized for microbiome composition has not been determined. In this study, we determined the reliable threshold level under which conclusions drawn from the data may be compromised. We also determined the type of microbial bias introduced by less-than-ideal genomic input.

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Environmental Temperatures Affect the Gastrointestinal Microbes of the Chinese Giant Salamander

Frontiers in Microbiology ◽

10.3389/fmicb.2021.543767 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lifeng Zhu ◽

Wei Zhu ◽

Tian Zhao ◽

Hua Chen ◽

Chunlin Zhao ◽

...

Keyword(s):

Potential Effect ◽

Shannon Index ◽

Effect Of Temperature ◽

Sample Type ◽

Gastrointestinal Microbiome ◽

Unifrac Distance ◽

Alpha And Beta Diversity ◽

Significant Difference ◽

Unweighted Unifrac ◽

Sample Time

An increasing number of studies have shown that warming also influences the animal gut microbiome (altering the community structure and decreasing its diversity), which might further impact host fitness. Here, based on an analysis of the stomach and gut (the entire intestine: from the anterior intestine to the cloaca) microbiome in laboratory larva of giant salamanders (Andrias davidianus) under different living water temperatures (5, 15, and 25°C) at two sample time points (80 and 330 days after the acclimation), we investigated the potential effect of temperature on the gastrointestinal microbiome community. We found the significant Interaction between sampling time and temperature, or type (stomach and gut) on Shannon index in the gastrointestinal microbiome of the giant salamanders. We also found the significant difference in Shannon index among temperature groups within the same sample type (stomach or gut) at each sample time. 10% of variation in microbiome community could be explained by temperature alone in the total samples. Both the stomach and gut microbiomes displayed the highest similarity in the microbiome community (significantly lowest pairwise unweighted Unifrac distance) in the 25-degree group between the two sampling times compared to those in the 5-degree and 15-degree groups. Moreover, the salamanders in the 25°C treatment showed the highest food intake and body mess compared to that of other temperature treatments. A significant increase in the abundance of Firmicutes in the gastrointestinal microbiome on day 330 with increasing temperatures might be caused by increased host metabolism and food consumption. Therefore, we speculate that the high environmental temperature might indirectly affect both alpha and beta diversity of the gastrointestinal microbiome.

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Protein utilisation by the mammary gland in lactating dairy cows

Proceedings of the British Society of Animal Production (1972) ◽

10.1017/s0308229600021267 ◽

1992 ◽

Vol 1992 ◽

pp. 1-1 ◽

Cited By ~ 1

Author(s):

J A Metcalf ◽

D E Beever ◽

J D Sutton ◽

D J Humphries

Keyword(s):

Mammary Gland ◽

Dry Matter ◽

Milk Composition ◽

Protein Levels ◽

Lactating Cows ◽

Lactating Dairy Cows ◽

Milk Output ◽

Underlying Mechanisms ◽

Protein Supply ◽

Friesian Cows

Milk output has been manipulated by dietary methods for many years, however the underlying mechanisms for changes in milk composition are as yet unclear. In an attempt to further understand these mechanisms we have compared the mammary uptake of metabolites on two isoenergetic diets with different protein levels expected to provide different amounts of amino acid to the mammary gland.Early- to mid-lactation Friesian cows were used to examine the effect of increased dietary protein supply on the supply of metabolites to and uptake by the mammary gland in relation to milk protein synthesis. Two barley based concentrates were formulated to contain 20.8 (Cl) or 29.1 (C2) g N/kg DM, using fishmeal (Provimi 66, high UDP) as the supplementary protein and fed with grass silage (28.3 g N/kg DM) at a total dry matter intake of 17 kg/day. In Experiment 1 these diets were fed at 50:50 (concentrate:silage) to four lactating cows fitted with rumen and duodenal cannulae in a simple crossover design.

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Breast Milk, a Source of Beneficial Microbes and Associated Benefits for Infant Health

Nutrients ◽

10.3390/nu12041039 ◽

2020 ◽

Vol 12 (4) ◽

pp. 1039 ◽

Cited By ~ 11

Author(s):

Katríona E. Lyons ◽

C. Anthony Ryan ◽

Eugene M. Dempsey ◽

R. Paul Ross ◽

Catherine Stanton

Keyword(s):

Mammary Gland ◽

Breast Milk ◽

Human Milk ◽

Infant Health ◽

Gastrointestinal Disease ◽

Newborn Infants ◽

Human Breast Milk ◽

Microbial Composition ◽

Beneficial Microbes ◽

Health And Nutrition

Human breast milk is considered the optimum feeding regime for newborn infants due to its ability to provide complete nutrition and many bioactive health factors. Breast feeding is associated with improved infant health and immune development, less incidences of gastrointestinal disease and lower mortality rates than formula fed infants. As well as providing fundamental nutrients to the growing infant, breast milk is a source of commensal bacteria which further enhance infant health by preventing pathogen adhesion and promoting gut colonisation of beneficial microbes. While breast milk was initially considered a sterile fluid and microbes isolated were considered contaminants, it is now widely accepted that breast milk is home to its own unique microbiome. The origins of bacteria in breast milk have been subject to much debate, however, the possibility of an entero-mammary pathway allowing for transfer of microbes from maternal gut to the mammary gland is one potential pathway. Human milk derived strains can be regarded as potential probiotics; therefore, many studies have focused on isolating strains from milk for subsequent use in infant health and nutrition markets. This review aims to discuss mammary gland development in preparation for lactation as well as explore the microbial composition and origins of the human milk microbiota with a focus on probiotic development.

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Zinc supplementation ameliorates lung injury by reducing neutrophil recruitment and activity

Thorax ◽

10.1136/thoraxjnl-2019-213357 ◽

2020 ◽

Vol 75 (3) ◽

pp. 253-261 ◽

Cited By ~ 6

Author(s):

Inga Wessels ◽

Johanna Theresa Pupke ◽

Klaus-Thilo von Trotha ◽

Alexander Gombert ◽

Anika Himmelsbach ◽

...

Keyword(s):

Lung Injury ◽

Zinc Supplementation ◽

Inflammatory Diseases ◽

Risk Groups ◽

Lavage Fluid ◽

Neutrophil Recruitment ◽

Polymorphonuclear Neutrophils ◽

Lung Damage ◽

Inflammatory Status

IntroductionZinc is well known for its anti-inflammatory effects, including regulation of migration and activity of polymorphonuclear neutrophils (PMN). Zinc deficiency is associated with inflammatory diseases such as acute lung injury (ALI). As deregulated neutrophil recruitment and their hyper-activation are hallmarks of ALI, benefits of zinc supplementation on the development of lipopolysaccharides (LPS)-induced ALI were tested.Methods64 C57Bl/6 mice, split into eight groups, were injected with 30 µg zinc 24 hours before exposure to aerosolised LPS for 4 hours. Zinc homoeostasis was characterised measuring serum and lung zinc concentrations as well as metallothionein-1 expression. Recruitment of neutrophils to alveolar, interstitial and intravascular space was assessed using flow cytometry. To determine the extent of lung damage, permeability and histological changes and the influx of protein into the bronchoalveolar lavage fluid were measured. Inflammatory status and PMN activity were evaluated via tumour necrosis factor α levels and formation of neutrophil extracellular traps. The effects of zinc supplementation prior to LPS stimulation on activation of primary human granulocytes and integrity of human lung cell monolayers were assessed as well.ResultsInjecting zinc 24 hours prior to LPS-induced ALI indeed significantly decreased the recruitment of neutrophils to the lungs and prevented their hyperactivity and thus lung damage was decreased. Results from in vitro investigations using human cells suggest the transferability of the finding to human disease, which remains to be tested in more detail.ConclusionZinc supplementation attenuated LPS-induced lung injury in a murine ALI model. Thus, the usage of zinc-based strategies should be considered to prevent detrimental consequences of respiratory infection and lung damage in risk groups.

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Faecal microbiota transplantation from metabolically compromised human donors accelerates osteoarthritis in mice

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2019-216471 ◽

2020 ◽

Vol 79 (5) ◽

pp. 646-656 ◽

Cited By ~ 2

Author(s):

ZeYu Huang ◽

Jing Chen ◽

BoLei Li ◽

Benhua Zeng ◽

Ching-Heng Chou ◽

...

Keyword(s):

Metabolic Syndrome ◽

Gut Microbiome ◽

Joint Damage ◽

The Other ◽

Gut Permeability ◽

Microbial Composition ◽

Germ Free ◽

Knee Oa ◽

Inflammatory Protein ◽

Faecal Samples

ObjectivesEmerging evidence suggests that the microbiome plays an important role in the pathogenesis of osteoarthritis (OA). We aimed to test the two-hit model of OA pathogenesis and potentiation in which one ‘hit’ is provided by an adverse gut microbiome that activates innate immunity; the other ‘hit’ is underlying joint damage.MethodsMedical history, faecal and blood samples were collected from human healthy controls (OA-METS-, n=4), knee OA without metabolic syndrome (OA+METS-, n=7) and knee OA with metabolic syndrome (OA+METS+, n=9). Each group of human faecal samples, whose microbial composition was identified by 16S rRNA sequencing, was pooled and transplanted into germ-free mice 2 weeks prior to meniscal/ligamentous injury (MLI) (n≥6 per group). Eight weeks after MLI, mice were evaluated for histological OA severity and synovitis, systemic inflammation and gut permeability.ResultsHistological OA severity following MLI was minimal in germ-free mice. Compared with the other groups, transplantation with the OA+METS+ microbiome was associated with higher mean systemic concentrations of inflammatory biomarkers (interleukin-1β, interleukin-6 and macrophage inflammatory protein-1α), higher gut permeability and worse OA severity. A greater abundance of Fusobacterium and Faecalibaterium and lesser abundance of Ruminococcaceae in transplanted mice were consistently correlated with OA severity and systemic biomarkers concentrations.ConclusionThe study clearly establishes a direct gut microbiome-OA connection that sets the stage for a new means of exploring OA pathogenesis and potentially new OA therapeutics. Alterations of Fusobacterium, Faecalibaterium and Ruminococcaceae suggest a role of these particular microbes in exacerbating OA.

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The shrimp superfamily Sergestoidea: a global phylogeny with definition of new families and an assessment of the pathways into principal biotopes

Royal Society Open Science ◽

10.1098/rsos.170221 ◽

2017 ◽

Vol 4 (9) ◽

pp. 170221 ◽

Cited By ~ 6

Author(s):

A. L. Vereshchaka

Keyword(s):

Phylogenetic Analysis ◽

Vertical Direction ◽

Evolutionary Model ◽

Copulatory Organ ◽

Morphological Characters ◽

Valid Species ◽

Genus Level ◽

Family Level ◽

Medium Level ◽

Definition Of

The phylogenetic analysis of Sergestoidea based on 253 morphological characters and encompassing all 99 valid species confirmed all previously recognized genus-level clades. Analysis retrieved five major robust clades that correspond to families Luciferidae, Sergestidae, Acetidae fam.n., Sicyonellidae fam.n. and Petalidiumidae fam.n. Synonymy, emended diagnoses and composition of revealed family-level clades are provided. Three types of morphological characters were important in the phylogeny of the Sergestoidea: general external characters, copulatory organs, and photophores. Novel metrics to quantify the contribution of these character types were tested. General external characters were significant in supporting the major clades (80% of the families and nearly half of the genera). Copulatory organ characters and photophores greatly supported the medium-level clades: Lucifer, Belzebub , Petalidium, Neosergestes, Challengerosergia (copulatory organ characters) and Lucensosergia , Challengerosergia, Gardinerosergia , Phorcosergia (photophores). An evolutionary model of the Sergestoidea showing their pathways into their principal biotopes is proposed: the major clades evolved in a vertical direction (from epi- to bathypelagic); further divergence at the genus level occurred within vertical zones in a horizontal direction, with the invasion of the benthopelagic and neritic (shelf and estuarine) habitats and speciation within these domains.

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Pollen Analysis of the Honeys Samples Produced in the Three Phyto-geographical Zones of Benin

European Scientific Journal ESJ ◽

10.19044/esj.2017.v13n18p528 ◽

2017 ◽

Vol 13 (18) ◽

pp. 528 ◽

Cited By ~ 1

Author(s):

François Ezin Azonwade ◽

Armand Paraïso ◽

Monique G. Tossou ◽

Haziz Sina ◽

Aude Eminsede Kelomey ◽

...

Keyword(s):

Zea Mays ◽

Plant Species ◽

Pollen Analysis ◽

Parkia Biglobosa ◽

Genus Level ◽

Pollen Content ◽

Family Level ◽

Conventional Methods ◽

Sudanian Zone ◽

Dry And Rainy Seasons

The aim of this work was the melissopalynologycal analysis of the honey samples collected both during the dry and rainy seasons of the three phyto-geographical zones of Benin. The analysis was performed by conventional methods on 60 honeys samples. The total of 138 taxa have been identified at family level (31), genus level (20) and to the level species (87). The number of pollens counted varies according to the phyto-geographical zones. Thus, 17091 pollens have been counted in the samples of the Sudanian zone; 13884 in those of the Sudano-Guinean zone and 7960 pollens in those of the Guinean zone. The pollen content of the honey samples reflects the plant species of the three phyto-geographical zones. The most dominant plant taxa were Combretaceaes (26.01%) and Parkia biglobosa (10.67%) in Sudanian zone, Combretaceae (29.52%) in SudanoGuinean zone. In the Guinean zone, the dominant taxa were Zea mays (18.35%) and Terminalia (15.34%). The specific richness varies from 6 to 43 in the Sudanian zone, from 7 to 34 in the Sudano-Guinean zone and from 1 to 28 taxa in the Guinean zone. None of the density of the dominant pollens reached 45%, thus all the analyzed honeys are polyfloral.

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Effect of High-Fat Diet on the Intestinal Flora in Letrozole-Induced Polycystic Ovary Syndrome Rats

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/6674965 ◽

2021 ◽

Vol 2021 ◽

pp. 1-13

Author(s):

Yan-Hua Zheng ◽

Ying Xu ◽

Hong-Xia Ma ◽

Cheng-Jie Liang ◽

Tong Yang

Keyword(s):

Polycystic Ovary Syndrome ◽

Polycystic Ovary ◽

Intestinal Flora ◽

High Fat ◽

Microbial Composition ◽

Ovary Syndrome ◽

Linear Discriminant ◽

Regular Diet ◽

Inflammatory Status ◽

Α Diversity

Aim. The aim of this study was to explore whether letrozole and high-fat diets (HFD) can induce obese insulin-resistant polycystic ovary syndrome (PCOS) with intestinal flora dysbiosis in a rat model. We compared the changes in the intestinal flora of letrozole-induced rats fed with HFD or normal chow, to explore the effects of HFD and letrozole independently and synergistically on the intestinal flora. Methods. Five-week-old female Sprague Dawley (SD) rats were divided into four groups: control (C) group fed with regular diet; L1 group administered with letrozole and fed with regular diet; L2 group received letrozole and fed with HFD; and HFD group fed with HFD. At the end of the experiment, ovarian morphology, hormones, metabolism, oxidative stress, and inflammatory status of all rats were studied. 16S rDNA high-throughput sequencing was used to profile microbial communities, and various multivariate analysis approaches were used to quantitate microbial composition, abundance, and diversity. Results. Compared to the C group, the increased plasma fasting insulin and glucose, HOMA-IR, triglyceride, testosterone, and malondialdehyde were significantly higher in the L2 group, while high-density lipoprotein cholesterol was significantly lower in the L1 group and L2 group. The indices of Chao1 and the Abundance-based Coverage Estimator (ACE) (α-diversity) in the L2 and HFD groups were significantly lower than that in the C group. Bray–Curtis dissimilarity based principal coordinate analysis (PCoA) plots and analysis of similarities (ANOSIM) test showed obvious separations between the L2 group and C group, between the HFD group and C group, and between the L2 and HFD groups. At the phylum level, Firmicutes and ratio of Firmicutes and Bacteroidetes (F/B ratio) were increased in the L2 group; Bacteroidetes was decreased in the L2 and HFD groups. No significant differences in bacterial abundance between the C group and L1 group were observed at the phylum level. Based on linear discriminant analysis (LDA) effect size (LEfSe) analysis, the bacterial genera (the relative abundance > 0.1%, LDA > 3, p < 0.05 ) were selected as candidate bacterial signatures. They showed that the abundance of Vibrio was significantly increased in the L1 group; Bacteroides and Phascolarctobacterium were enriched in the HFD group, and Bacteroides, Phascolarctobacterium, Blautia, Parabacteroides, Akkermansia [Ruminococcus]_torques_group, and Anaerotruncus were enriched in the L2 group. Conclusion. The effect of letrozole on intestinal flora was not significant as HFD. HFD could destroy the balance of intestinal flora and aggravate the intestinal flora dysbiosis in PCOS. Letrozole-induced rats fed with HFD have many characteristics like human PCOS, including some metabolic disorders and intestinal flora dysbiosis. The dysbiosis was characterized by an increased Firmicutes/Bacteroidetes ratio, an expansion of Firmicutes, a contraction of Bacteroidetes, and the decreased microbial richness. Beta-diversity also showed significant differences in intestinal microflora, compared with control rats.

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