scholarly journals Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Jolinda Pollock ◽  
Susannah J. Salter ◽  
Rebecca Nixon ◽  
Michael R. Hutchings
Keyword(s):  
Dairy Cattle ◽  
Antimicrobial Agents ◽  
Bacterial Load ◽  
Treatment Protocol ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Milk Samples ◽  
Antimicrobial Usage ◽  
Significant Difference ◽  
Contamination Effects

Abstract Background The blanket usage of antimicrobials at the end of lactation (or “drying off”) in dairy cattle is under increasing scrutiny due to concerns about antimicrobial resistance. To lower antimicrobial usage in dairy farming, farmers are now encouraged to use “selective dry cow therapy” whereby only cows viewed as at high risk of mastitis are administered antimicrobial agents. It is important to gain a better understanding of how this practice affects the udder-associated microbiota and the potential knock-on effects on antimicrobial-resistant bacterial populations circulating on the farm. However, there are challenges associated with studying low biomass environments such as milk, due to known contamination effects on microbiome datasets. Here, we obtained milk samples from cattle at drying off and at calving to measure potential shifts in bacterial load and microbiota composition, with a critical assessment of contamination effects. Results Several samples had no detectable 16S rRNA gene copies and crucially, exogenous contamination was detected in the initial microbiome dataset. The affected samples were removed from the final microbiome analysis, which compromised the experimental design and statistical analysis. There was no significant difference in bacterial load between treatments (P > 0.05), but load was lower at calving than at drying off (P = 0.039). Escherichia coli counts by both sequence and culture data increased significantly in the presence of reduced bacterial load and a decreasing trend of microbiome richness and diversity. The milk samples revealed diverse microbiomes not reflecting a typical infection profile and were largely comprised of gut- and skin-associated taxa, with the former decreasing somewhat after prolonged sealing of the teats. Conclusions The drying off period had a key influence on microbiota composition and bacterial load, which appeared to be independent of antimicrobial usage. The interactions between drying off treatment protocol and milk microbiome dynamics are clearly complex, and our evaluations of these interactions were restricted by low biomass samples and contamination effects. Therefore, our analysis will inform the design of future studies to establish whether different selection protocols could be implemented to further minimise antimicrobial usage.

scholarly journals Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yan Hui ◽  
Paulina Tamez-Hidalgo ◽  
Tomasz Cieplak ◽  
Gizaw Dabessa Satessa ◽  
Witold Kot ◽  
...  
Keyword(s):  
Immune Modulation ◽  
Amplicon Sequencing ◽  
Saccharina Latissima ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Colon Mucosa ◽  
Weaned Piglets ◽  
Brown Macroalgae ◽  
Blood Concentrations ◽  
Significant Difference

Abstract Background The direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders. Results This study investigated the effect of using rapeseed-seaweed blend (rapeseed meal added two brown macroalgae species Ascophylum nodosum and Saccharina latissima) fermented by lactobacilli (FRS) as feed ingredients in piglet weaning. From d 28 of life to d 85, the piglets were fed one of three different feeding regimens (n = 230 each) with inclusion of 0%, 2.5% and 5% FRS. In this period, no significant difference of piglet performance was found among the three groups. From a subset of piglets (n = 10 from each treatment), blood samples for hematology, biochemistry and immunoglobulin analysis, colon digesta for microbiome analysis, and jejunum and colon tissues for histopathological analyses were collected. The piglets fed with 2.5% FRS manifested alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier relative to the 0% FRS group. The colon microbiota composition was determined using V3 and V1-V8 region 16S rRNA gene amplicon sequencing by Illumina NextSeq and Oxford Nanopore MinION, respectively. The two amplicon sequencing strategies showed high consistency between the detected bacteria. Both sequencing strategies indicated that inclusion of FRS reshaped the colon microbiome of weaned piglets with increased Shannon diversity. Prevotella stercorea was verified by both methods to be more abundant in the piglets supplied with FRS feed, and its abundance was positively correlated with colonic mucosa thickness but negatively correlated with blood concentrations of leucocytes and IgG. Conclusions FRS supplementation relieved the gut lymphocyte infiltration of the weaned piglets, improved the colon mucosa barrier with altered microbiota composition. Increasing the dietary inclusion of FRS from 2.5% to 5% did not lead to further improvements.

scholarly journals Melatonin differences between day and night milk in primiparous holstein friesian and jersey dairy cattle

2021 ◽  
Author(s):  
Saim Boztepe ◽  
İsmail KESKIN ◽  
Ahmet SEMACAN ◽  
Fikret AKYUREK ◽  
İbrahim AYTEKIN ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Holstein Cows ◽  
New Production ◽  
Elisa Kit ◽  
Milk Samples ◽  
Holstein Friesian ◽  
Significant Difference ◽  
The Difference ◽  
Jersey Cows

Abstract This study was conducted to determine the levels of melatonin in the day and night milk of Holstein and Jersey cows. In the study, samples of daytime milk produced from 27 head of Holstein and 27 head of Jersey cows in the first lactation, which were raised in a private dairy cattle enterprise in the Kaşınhanı neighborhood of Meram district of Konya city Turkey, and night milk samples taken from the same cows that were blackened for one (1) week were used. Melatonin levels in milk samples taken from day and night milk were determined separately for Holstein and Jersey cows with the help of Bovine Melatonin (MLT) Elisa Kit. In the study, it was determined that the ratio of melatonin in day and night milk in Holstein cows was 2.912 pg/ml and 11.314 pg/ml, respectively, and the ratio of melatonin in Jersey cows was 2.924 pg/ml and 6.954 pg/ml in the same order. The difference between the melatonin levels of the day and night milk of Holstein and Jersey cows was found to be statistically significant (p<0.01). At the end of the study, it can be stated that night milk can be used for medical purposes and a new production source may arise for producers since there is a significant difference in melatonin between day and night milk.

scholarly journals Human milk microbiota in sub-acute lactational mastitis induces inflammation and undergoes changes in composition, diversity and load

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alba Boix-Amorós ◽  
Maria Teresa Hernández-Aguilar ◽  
Alejandro Artacho ◽  
Maria Carmen Collado ◽  
Alex Mira
Keyword(s):  
Epithelial Cell ◽  
Human Milk ◽  
Mammary Epithelial Cell ◽  
Clinical Symptoms ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Mammary Epithelial ◽  
Rrna Gene ◽  
Milk Samples ◽  
Acute Mastitis

Abstract Sub-acute mastitis (SAM) is a prevalent disease among lactating women, being one of the main reasons for early weaning. Although the etiology and diagnosis of acute mastitis (AM) is well established, little is known about the underlying mechanisms causing SAM. We collected human milk samples from healthy and SAM-suffering mothers, during the course of mastitis and after symptoms disappeared. Total (DNA-based) and active (RNA-based) microbiota were analysed by 16S rRNA gene sequencing and qPCR. Furthermore, mammary epithelial cell lines were exposed to milk pellets, and levels of the pro-inflammatory interleukin IL8 were measured. Bacterial load was significantly higher in the mastitis samples and decreased after clinical symptoms disappeared. Bacterial diversity was lower in SAM milk samples, and differences in bacterial composition and activity were also found. Contrary to AM, the same bacterial species were found in samples from healthy and SAM mothers, although at different proportions, indicating a dysbiotic ecological shift. Finally, mammary epithelial cell exposure to SAM milk pellets showed an over-production of IL8. Our work therefore supports that SAM has a bacterial origin, with increased bacterial loads, reduced diversity and altered composition, which partly recovered after treatment, suggesting a polymicrobial and variable etiology.

scholarly journals Alterations of lung microbiota in a mouse model of LPS-induced lung injury

2015 ◽  
Vol 309 (1) ◽  
pp. L76-L83 ◽  
Author(s):  
Valeriy Poroyko ◽  
Fanyong Meng ◽  
Angelo Meliton ◽  
Taras Afonyushkin ◽  
Alexander Ulanov ◽  
...  
Keyword(s):  
Lung Injury ◽  
Mouse Model ◽  
Lung Inflammation ◽  
Diversity Index ◽  
Bacterial Load ◽  
Rrna Gene ◽  
Barrier Dysfunction ◽  
Intratracheal Administration ◽  
Significant Difference ◽  
Community Complexity

Acute lung injury (ALI) and the more severe acute respiratory distress syndrome are common responses to a variety of infectious and noninfectious insults. We used a mouse model of ALI induced by intratracheal administration of sterile bacterial wall lipopolysaccharide (LPS) to investigate the changes in innate lung microbiota and study microbial community reaction to lung inflammation and barrier dysfunction induced by endotoxin insult. One group of C57BL/6J mice received LPS via intratracheal injection ( n = 6), and another received sterile water ( n = 7). Bronchoalveolar lavage (BAL) was performed at 72 h after treatment. Bacterial DNA was extracted and used for qPCR and 16S rRNA gene-tag (V3–V4) sequencing (Illumina). The bacterial load in BAL from ALI mice was increased fivefold ( P = 0.03). The community complexity remained unchanged (Simpson index, P = 0.7); the Shannon diversity index indicated the increase of community evenness in response to ALI ( P = 0.07). Principal coordinate analysis and analysis of similarity (ANOSIM) test ( P = 0.005) revealed a significant difference between microbiota of control and ALI groups. Bacteria from families Xanthomonadaceae and Brucellaceae increased their abundance in the ALI group as determined by Metastats test ( P < 0.02). In concordance with the 16s-tag data, Stenotrohomonas maltophilia ( Xanthomonadaceae) and Ochrobactrum anthropi ( Brucellaceae) were isolated from lungs of mice from both groups. Metabolic profiling of BAL detected the presence of bacterial substrates suitable for both isolates. Additionally, microbiota from LPS-treated mice intensified IL-6-induced lung inflammation in naive mice. We conclude that the morbid transformation of ALI microbiota was attributed to the set of inborn opportunistic pathogens thriving in the environment of inflamed lung, rather than the external infectious agents.

scholarly journals Influence of intramuscular depot-medroxyprogesterone acetate initiation on vaginal microbiota in the postpartum period

2020 ◽  
Author(s):  
Bridget M Whitney ◽  
Sujatha Srinivasan ◽  
Kenneth Tapia ◽  
Eric Munene Muriuki ◽  
Bhavna H Chohan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Medroxyprogesterone Acetate ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Bacterial Load ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Nugent Score ◽  
Depot Medroxyprogesterone Acetate ◽  
Significant Difference

Abstract Background The vaginal microbiome plays a key role in women’s reproductive health. Use of exogenous hormones, such as intramuscular depot-medroxyprogesterone acetate (DMPA-IM), may alter the composition of vaginal bacterial community. Methods Vaginal swabs were collected from postpartum Kenyan women initiating DMPA-IM or non-hormonal contraception (non-HC). Bacterial vaginosis was assessed by Nugent score (Nugent-BV) and bacterial community composition was evaluated using broad-range 16S rRNA gene PCR with high-throughput sequencing. Changes in Nugent score, alpha diversity (Shannon diversity index), and total bacterial load between contraceptive groups from enrollment to three-months post-initiation were estimated using multivariable linear mixed effects regression. Results Among 54 HIV-negative women, 33 choosing DMPA-IM and 21 choosing non-HC, Nugent-BV was more common among DMPA-IM users at enrollment. At follow-up, Nugent score had decreased significantly among DMPA-IM users (Δ=-1.89 (95%CI:-3.53, -0.25; p=0.02) while alpha diversity remained stable (Δ=0.03, 95%CI:-0.24, 0.30; p=0.83). Conversely, Nugent score remained relatively stable among non-HC users (Δ=-0.73, 95%CI:-2.18, 0.73; p=0.33) while alpha diversity decreased (Δ=-0.34, 95%CI:-0.67, -0.001; p=0.05). Total bacterial load decreased slightly in DMPA-IM users and increased slightly among non-HC users, resulting in a significant difference in change between the contraceptive groups (difference=-0.64 log10 gene copies/swab, 95%CI:-1.19, -0.08; p=0.02). While significant changes in Nugent score and alpha diversity were observed within contraceptive groups, changes between groups were not significantly different. Conclusions Postpartum vaginal bacterial diversity did not change in DMPA-IM users despite a reduction in Nugent-BV, but decreased significantly among women using non-HC. Choice of contraception may influence Lactobacillus recovery in postpartum women.

The Effect of Holder Pasteurization on the Diversity of the Human Milk Bacterial Microbiota Using High-Throughput DNA Sequencing

2021 ◽  
pp. 089033442110119
Author(s):  
Igrid García-González ◽  
Karina Corona-Cervantes ◽  
Fernando Hernández-Quiroz ◽  
Loan Edel Villalobos-Flores ◽  
Flor Galván-Rodríguez ◽  
...  
Keyword(s):  
Human Milk ◽  
Bacterial Diversity ◽  
High Throughput ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Sequencing Data ◽  
Cross Sectional ◽  
Milk Samples ◽  
Bacterial Microbiota ◽  
Before And After

Background Human milk is the best food for infants; however, when breastfeeding is not possible, pasteurized milk from human milk banks is the best alternative. Little has been reported about variations in the bacterial microbiota composition of human milk after pasteurization. Research aim To characterize and compare the bacterial microbiota composition and diversity within human milk among Mexican mothers before and after the Holder pasteurization process. Methods: A cross-sectional, observational, and comparative design was used. The effect of the pasteurization process on the bacterial composition and diversity of human milk samples of donors ( N = 42) from a public milk bank was assessed before and after pasteurization by high throughput deoxyribonucleic acid sequencing of V3-16S rRNA gene libraries. Sequencing data were examined using the Quantitative Insights into Microbial Ecology software and Phyloseq in R environment. Results A varied community of bacteria was found in both raw and pasteurized human milk. The bacterial diversity of the milk samples was increased by the pasteurization, where some thermoduric bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were more abundant. The source tracker analysis indicated that at most 1.0% of bacteria may have come from another source, showing the safety of the process used to treat milk samples. Conclusion The pasteurization process increased the bacterial diversity. We selected taxa capable of surviving the process, which could proliferate after the treatment without being a risk for infants.

scholarly journals Microbial assessment of milk collected from different markets of Mymensingh, Gazipur and Sherpur districts of Bangladesh and determination of antimicrobial resistance patterns of the isolated bacteria

2017 ◽  
Vol 1 (1) ◽  
pp. 7-16
Author(s):  
Mohammad Farhad Hossain ◽  
Md Tanvir Rahman ◽  
SM Lutful Kabir
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Load ◽  
Microbiological Quality ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Selective Media ◽  
E Coli ◽  
Milk Samples ◽  
Unpasteurized Milk

The study was conducted to determine the total viable count (TVC) and total coliform count (TCC) of unpasteurized, pasteurized and UHT milk samples to assess their microbiological quality. A total of 60 milk samples were collected from different markets of Mymensingh, Gazipur and Sherpur districts. The TVC of milk was performed to determine the bacterial load in supplied milk samples and TCC to determine the coliform bacterial load in collected milk samples. Milk samples were cultured onto various selective media for the isolation of bacteria. The isolated bacteria were identified by cultural properties on different selective media, biochemical tests and finally by PCR. Out of 60 samples 20 unpasteurized milk samples from different markets were found positive for Staphylococcus aureus and 19 unpasteurized milk samples were found positive for Escherichia coli. All the S. aureus were found positive for S. aureus specific 16S rRNA gene by PCR. Out of 19 isolates of E. coli, 15 were found positive for E. coli 16S rRNA gene by PCR. Results of antimicrobial susceptibility test showed that most of the isolates of S. aureus and E .coli were susceptible to azithromycin, streptomycin, gentamicin, norfloxacin, tetracycline and ciprofloxacin but resistant to amoxicillin and erythromycin. The findings of this study revealed the presence of multidrug resistant S. aureus and E. coli in unpasteurized milk samples that posseses a serious threat to public health. Asian Australas. J. Food Saf. Secur. 2017, 1 (1), 7-16

scholarly journals Effects of Different Estrous Synchronization Methods on the Composition of Simmental Cow’s Milk

2017 ◽  
Vol 45 (1) ◽  
pp. 7 ◽  
Author(s):  
Ibrahim Seker ◽  
Ali Risvanli ◽  
Mehmet Calicioglu ◽  
Gokhan Kursad Incili ◽  
Nevzat Saat
Keyword(s):  
Dairy Cattle ◽  
Milk Fat ◽  
Management Practices ◽  
Primary Objective ◽  
Control Group ◽  
Lactation Period ◽  
Estrous Synchronization ◽  
Milk Samples ◽  
Significant Difference ◽  
The Difference

Background: Estrous synchronization is one of the primary applications performed to improve the fertility and to consolidate the parturition times in dairy cattle farms. Since the primary objective is to increase fertility regardless of the method of synchronization used, the effect of this process on the udder health and the quality of milk is generally ignored. Therefore, in the present study, the aim was to investigate the effect of different estrous synchronization methods t on the milk quality in a dairy cattle farm.Materials, Methods & Results: In this study, a total of 100 Simmental cows the same farm under good management practices were used. The animals were randomly divided into 4 groups of 25 cows each. The animals in the 1st group were used as a control group without any treatment. Progesterone-releasing intravaginal device (PRID) was inserted to the animals in the 2nd group, double dose of prostaglandin F2 alpha (PGF2-alpha) with 11 days apart was applied to the animals in the 3rd group, and the Ovsynch protocol was applied to the animals in the 4th group. Starting from the first day of the applications, milk samples from each milk tank belonging to the groups were taken, kept frozen for 3 months and analyzed for the levels of fat, nonfat solids, density, protein, lactose and minerals over the course of one month. According to the results, the minimum milk fat content was found in the PRID group as 2.47 ± 0.354%, and the highest value was in the PGF2-alpha group as 3.58 ± 0.207%. The difference in milk fat ratio between the groups was found to be significant (P < .05). However, the differences between the groups for other parameters were not significant (P > .05).Discussion: Among the reasons for the low values of the milk fat rates obtained in the present study than the mean values of all lactation milk fat rates of the Simmental breed, the effect of the lactation period in which the milk samples were collected comes to mind. Because, as we know, the first 45-60 day period following the start of lactation after parturition in cattle is accepted as the period in which daily milk yield reaches to the maximum level of the lactation period. This period lasts for a certain period of time, and then starts to decrease gradually. Among the non-hereditary factors, the most important factor causing changes in the composition of the milk and its amount is the lactation period. In this study, the significant difference in the milk fat rates between the control and the application groups is quite remarkable compared to the low level of milk fat rates in the milk in all groups. According to the multiple comparison test results to determine which groups these differences arise from, the difference was found to be particularly between the PGF2-alpha group and PRID group. In this study, no significant effects of different synchronization methods on all components of the milk except the milk fat and the density values were determined. But results indicate that Ovsynch group was the synchronization group that caused the minimum change in milk fat compared to the other groups.

scholarly journals Profiling Branchial Bacteria of Atlantic Salmon (Salmo salar L.) Following Exposure to Antimicrobial Agents

2021 ◽  
Vol 2 ◽  
Author(s):  
Joel Slinger ◽  
James W. Wynne ◽  
Mark B. Adams
Keyword(s):  
Atlantic Salmon ◽  
Antimicrobial Agents ◽  
Bacterial Load ◽  
Taxonomic Diversity ◽  
Antimicrobial Treatment ◽  
Post Treatment ◽  
Rrna Gene ◽  
Area Of Concern ◽  
Antimicrobial Treatments

Microbial gill diseases caused by either opportunistic or specific pathogens are an emerging area of concern for aquaculture producers in part due to their sometimes complex and/or cryptic nature. Many antimicrobial treatments used in aquacultural settings are broad spectrum in nature. The effect of such therapeutics upon reduction and recolonization of commensal or pathogenic microbiota post-treatment has received little attention to date. Commensal bacteria are an integral component of the barrier function of mucosal surfaces in animals. This study evaluated the effect of several commercially relevant antimicrobial treatments upon the diversity and composition of branchial bacteria of Atlantic salmon. Here we exposed Atlantic salmon smolt to a number of commercially relevant antimicrobial treatments including chemotherapeutants (chloramine-t and hydrogen peroxide) and antibiotics (oxytetracycline and florfenicol) in vivo. Subsequently we examined the change in bacterial load, 16S rRNA gene expression, and taxonomic diversity post-treatment upon the gills. Results revealed a decrease in cultivable bacterial colonies after antimicrobial treatment, and a downstream decrease in bacterial richness and abundance post-treatment, with colonization of several prominent pathogenic taxa including Vibrio and Tenacibaculum. Temporal tracing over a 14-day period demonstrated that the bacteriome of gill mucus is sensitive to change, and altered by antimicrobial treatment and handling. This study identified candidate antimicrobial treatments which could be implemented in future studies to illustrate the effect of dysbiosis on microbial gill diseases.

scholarly journals Analysis of the developing gut microbiota in young dairy calves—impact of colostrum microbiota and gut disturbances

2020 ◽  
Vol 53 (1) ◽  
Author(s):  
Bui Phan Thu Hang ◽  
Ewa Wredle ◽  
Johan Dicksved
Keyword(s):  
Average Daily Gain ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
Fecal Samples ◽  
Calf Health ◽  
Significant Difference

AbstractThe aim of this study was to characterize the colostrum and fecal microbiota in calves and to investigate whether fecal microbiota composition was related to colostrum microbiota or factors associated with calf health. Colostrum samples were collected in buckets after hand milking of 76 calving cows from 38 smallholder dairy farms. Fecal samples were taken directly from the rectum of 76 calves at birth and at 14 days age. The bacterial community structure in colostrum and feces was analyzed by terminal restriction fragment length polymorphism for all samples, and the microbial composition was determined by 16S rRNA gene amplicon sequencing for a subset of the samples (8 colostrum, 40 fecal samples). There was a significant difference in fecal microbiota composition between day 0 and day 14 samples, but no associations between the microbiota and average daily gain, birth weight, or transfer of passive immunity. At 14 days of age, Faecalibacterium and Butyricicoccus were prevalent in higher relative abundances in the gut of healthy calves compared to calves with diarrhea that had been treated with antimicrobials. Colostrum showed great variation in composition of microbiota but no association to fecal microbiota. This study provides the first insights into the composition of colostrum and fecal microbiota of young dairy calves in southern Vietnam and can form the basis for future more detailed studies.

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