Nasal and gut microbiota for sows of different health status within six commercial swine farms from one swine production system

AbstractSow culling is an essential practice in swine herds to optimize animal health and productivity; and cull sows represent a considerable proportion of the herd at any given time point. Even though recent studies have reported that the microbiome is associated with susceptibility to diseases, the microbiome in the cull sow population has not been explored. The main objective of this study was to investigate whether there were differences in abundance and diversity of microbes encountered in the gut and upper respiratory tract of sows of different health status (healthy, cull, and compromised cull sows) and different farms. Farms were visited once, 30 individual fecal and nasal swab samples were obtained per farm; and pooled across animals by health status and farm in pools of five. Genomic DNA was extracted and samples were subjected to MiSeq 16S rRNA sequencing using Illumina MiSeq. Diversity analyses were conducted using QIIME. Alpha diversity was analyzed using observed OTUs, PD Whole Tree, and Chao1; and beta diversity was assessed using weighted UniFrac. The mean number of OTUs was 3,846.97±9,078.87 and 28,747.92±14,090.50 for nasal and fecal pooled samples, respectively. Diversity of the nasal microbiota was low compared to the gut microbiota. For nasal samples, there was a difference in diversity between samples from farms 1-6 using the Chao1 metric (p = 0.0005); and weighted beta diversity values indicated clustering by health status. For fecal samples, there was no difference in diversity between compromised, cull, and healthy sows; or between samples from farms 1-6. Weighted PCoA analyses showed an influence of farm of origin on the diversity of pooled fecal samples. Finally, differences at the genus level were found in the fecal microbiota composition of sows of different health status and farm of origin; but not for nasal microbiota.

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A cross-sectional study of the nasal and fecal microbiota of sows from different health status within six commercial swine farms

PeerJ ◽

10.7717/peerj.12120 ◽

2021 ◽

Vol 9 ◽

pp. e12120

Author(s):

Andreia G. Arruda ◽

Loic Deblais ◽

Vanessa L. Hale ◽

Christopher Madden ◽

Monique Pairis-Garcia ◽

...

Keyword(s):

Health Status ◽

Alpha Diversity ◽

Fecal Microbiota ◽

Rrna Gene ◽

Microbiota Composition ◽

Upper Respiratory Tract ◽

Microbial Composition ◽

Cross Sectional ◽

Swine Farms ◽

Nasal Microbiota

Background Cull sows are a unique population on swine farms, often representing poor producing or compromised animals, and even though recent studies have reported that the microbiome is associated with susceptibility to diseases, the microbiome of the cull sow population has not been explored. The main objective of this study was to investigate whether there were differences in fecal and upper respiratory tract microbiota composition for groups of sows of different health status (healthy, cull, and compromised/ clinical sows) and from different farms (1 to 6). Methods Six swine farms were visited once. Thirty individual fecal samples and nasal swabs were obtained at each farm and pooled by five across health status and farm. Samples underwent 16S rRNA gene amplicon sequencing and nasal and fecal microbiota were analyzed using QIIME2 v.2021.4. Results Overall, the diversity of the nasal microbiota was lower than the fecal microbiota (p < 0.01). No significant differences were found in fecal or nasal alpha diversity by sow’s health status or by farm. There were significant differences in nasal microbial composition by farm and health status (PERMANOVA, p < 0.05), and in fecal microbiota by farm (PERMANOVA, p < 0.05), but not by health status. Lastly, at the L7 level, there was one differentially abundant taxa across farms for each nasal and fecal pooled samples. Discussion This study provided baseline information for nasal and fecal microbiota of sows under field conditions, and results suggest that farm of origin can affect microbial diversity and composition. Furthermore, sow’s health status may have an impact on the nasal microbiota composition.

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Fecal Bacterial Communities Differ by Lactation Status in Post-Partum Women and Their Infants

Journal of Human Lactation ◽

10.1177/08903344211060343 ◽

2021 ◽

pp. 089033442110603

Author(s):

Eliot N. Haddad ◽

Lynn E. Ferro ◽

Kathleen E. B. Russell ◽

Kameron Y. Sugino ◽

Jean M. Kerver ◽

...

Keyword(s):

Body Mass Index ◽

Gut Microbiota ◽

Human Milk ◽

Body Mass ◽

Beta Diversity ◽

Bifidobacterium Longum ◽

Univariate Analysis ◽

Body Mass Index Category ◽

Fecal Samples ◽

Milk Feeding

Background: Previous research examined effects of human milk on the infant gut microbiota, but little attention has been given to the microbiota of lactating women. Research Aim: To determine associations between exclusive human milk feeding and gut microbiota characteristics in mothers and infants at 6-weeks postpartum. Methods: A sample of mother–infant dyads ( N = 24) provided fecal samples and questionnaire responses at 6-weeks postpartum as part of the Pregnancy, EAting & POstpartum Diapers study. Deoxyribonucleic acid was extracted from stool samples, followed by (V4) 16S ribosomal ribonucleic acid gene amplicon sequencing. Alpha and beta diversity, in addition to taxa differences, were compared by human milk exposure status, exclusive versus non-exclusive. A subset of dyads (those exclusively fed human milk; n = 14) was analyzed for shared bifidobacterial species using polymerase chain reaction. Results: Alpha diversity was significantly lower in exclusively human milk-fed infants. Maternal lactation status (exclusive vs. partial) and Shannon diversity were associated in univariate analysis but were no longer associated in multivariable regression including body mass index category in the model. Beta diversity (Sorensen dissimilarity) of fecal samples from women and infants was significantly associated with human milk feeding. Of six infants with Bifidobacterium longum subspecies longum in their fecal samples, all their mothers shared the same species. Conclusion: Maternal gut microbiotas differ by lactation status, a relationship potentially confounded by body mass index category. Further research is needed to identify whether lactation directly influences the maternal gut microbiota, which may be another mechanism by which lactation influences health.

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Probiotic Supplementation in a Clostridium difficile-Infected Gastrointestinal Model Is Associated with Restoring Metabolic Function of Microbiota

Microorganisms ◽

10.3390/microorganisms8010060 ◽

2019 ◽

Vol 8 (1) ◽

pp. 60

Author(s):

Mohd Baasir Gaisawat ◽

Chad W. MacPherson ◽

Julien Tremblay ◽

Amanda Piano ◽

Michèle M. Iskandar ◽

...

Keyword(s):

Gut Microbiota ◽

Alpha Diversity ◽

Gastrointestinal Disorder ◽

Short Chain Fatty Acids ◽

Rrna Gene ◽

Metabolic Function ◽

Microbial Composition ◽

Single Strain ◽

Fecal Samples ◽

Metabolic Functions

Clostridium (C.) difficile-infection (CDI), a nosocomial gastrointestinal disorder, is of growing concern due to its rapid rise in recent years. Antibiotic therapy of CDI is associated with disrupted metabolic function and altered gut microbiota. The use of probiotics as an adjunct is being studied extensively due to their potential to modulate metabolic functions and the gut microbiota. In the present study, we assessed the ability of several single strain probiotics and a probiotic mixture to change the metabolic functions of normal and C. difficile-infected fecal samples. The production of short-chain fatty acids (SCFAs), hydrogen sulfide (H2S), and ammonia was measured, and changes in microbial composition were assessed by 16S rRNA gene amplicon sequencing. The C. difficile-infection in fecal samples resulted in a significant decrease (p < 0.05) in SCFA and H2S production, with a lower microbial alpha diversity. All probiotic treatments were associated with significantly increased (p < 0.05) levels of SCFAs and restored H2S levels. Probiotics showed no effect on microbial composition of either normal or C. difficile-infected fecal samples. These findings indicate that probiotics may be useful to improve the metabolic dysregulation associated with C. difficile infection.

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Gut microbiota composition is associated with narcolepsy type 1

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000000896 ◽

2020 ◽

Vol 7 (6) ◽

pp. e896

Author(s):

Alexandre Lecomte ◽

Lucie Barateau ◽

Pedro Pereira ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Bacterial Communities ◽

Beta Diversity ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Differential Abundance ◽

Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

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A Pilot Study to Determine the Gut Microbiota of Hong Kong Infants Fed with Breast-milk And/or Infant Formula (P11-101-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz048.p11-101-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Cited By ~ 1

Author(s):

Oi Yee Yeung ◽

Yuk Fan Ng ◽

Jiachi Chiou ◽

Man-sau Wong

Keyword(s):

Hong Kong ◽

Breast Milk ◽

Gut Microbiota ◽

Infant Formula ◽

Newborn Infants ◽

Alpha Diversity ◽

Gut Health ◽

Unifrac Distance ◽

Fecal Samples ◽

The Government

Abstract Objectives Gut microbiome in newborn infants affect their gut health and future development. The major nutrient sources for infants aged 2–4 months are breast-milk or infant formula, hence it is worth investigating whether exclusively breastfed or infant formula-fed does affect the early development of the gut microbiota communities. Metagenomics has been applied to analyse the infant fecal samples in the United State and some European countries, however, similar studies were limited in Asia and especially Hong Kong. Methods Three groups of infants aged 2–4 months which were exclusively breastfed (BF), exclusively infant formula-fed (IF) or mix-fed with breast-milk and infant formula (MF) were recruited. Genomic DNA from the fecal sample and breast-milk was extracted and subjected to 16S rRNA next-generation sequencing to understand the gut microbiota profile, the difference of microbiota diversity and community abundance in these three feeding groups. The sequencing results were processed using pipelines Mothur and Qiime2. Results Overall the breast-milk showed higher alpha-diversity than the fecal samples. The 3 predominant Phyla were Proteobacteria, Firmicutes and Bacteroidetes within the fecal samples from all feeding patterns while the 3 dominant Phyla were Firmicutes, Proteobacteria and Actinobacteria in the breastmilk. Higher abundance of the well-known immune-modulating Genera Bifidobacterium and Lactobacillus were found in the fecal samples of BF and MF groups than the IF group whereas IF group harboured highest abundance of Genus Clostridium among 3 fecal groups. A PCoA based on unweighted UniFrac distance showed that the microbiota from the breastmilk clustered and distinctly separated from those of fecal samples. Moreover, the microbiota of MF subjects were close to BF subjects from the PCoA analysis. Conclusions Our preliminary results suggested that partial feeding with breast-milk could still maintain the major gut community composition as in the BF group. Feeding pattern affect the gut microbiota in Hong Kong infants aged 2–4 month and probiotic genera Bifidobacterium and Lactobacillus were found in the breast-milk, and fecal samples of BF and MF groups. Funding Sources Health and Medical Research Fund, Food and Health Bureau, The Government of the Hong Kong Special Administrative Region.

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Human Milk Feeding Patterns at 6 Months of Age are a Major Determinant of Fecal Bacterial Diversity in Infants

Journal of Human Lactation ◽

10.1177/0890334420957571 ◽

2020 ◽

pp. 089033442095757

Author(s):

Kameron Y. Sugino ◽

Tengfei Ma ◽

Jean M. Kerver ◽

Nigel Paneth ◽

Sarah S. Comstock

Keyword(s):

Gut Microbiota ◽

Human Milk ◽

Beta Diversity ◽

Maternal Obesity ◽

Alpha Diversity ◽

Major Determinant ◽

Cross Sectional ◽

Alpha And Beta Diversity ◽

Infant Diet ◽

Milk Feeding

Background Maternal pre-pregnancy obesity and human milk feeding have been associated with altered infant gut microbiota. Research aim Determine the relationships between maternal pre-pregnancy BMI, human milk exposure, and their influence on the infant microbiota simultaneously. Methods This was a cross-sectional study of infants at 6 months of age ( N = 36), a time when many infants are fed a mixed diet of human milk and other foods. Fecal samples and participant information were collected from a subset of dyads enrolled in two related prospective cohorts (ARCHGUT and BABYGUT) in Michigan. Sequencing the V4 region of the 16S gene was used to analyze fecal bacterial samples collected from 6-month-old infants. Participants were grouped into four categories designated by their extent of human milk exposure (100%, 80%, 50%–80%, ≤ 20% human milk in the infant diet) and by maternal pre-pregnancy BMI category (normal, overweight, obese). Results Fewer participants with pre-pregnancy obesity were breastfeeding at 6 months postpartum compared to non-obese participants (35.7% and 81.8%, respectively). In univariate analyses, maternal pre-pregnancy BMI and human milk exposure were both significantly associated with alpha and beta diversity of the infant microbiota. However, in multivariate analyses, human milk exposure accounted for 20% of the variation in alpha diversity, but pre-pregnancy BMI was not significantly associated with any form of microbiota diversity. Conclusions The proportion of the infant diet that was human milk at 6 months was the major determinant of alpha and beta diversity of the infant. Maternal obesity contributes to the gut microbiota by its association with the extent of human milk feeding.

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Viral dysbiosis in children with new-onset celiac disease

PLoS ONE ◽

10.1371/journal.pone.0262108 ◽

2022 ◽

Vol 17 (1) ◽

pp. e0262108

Author(s):

Mohammad El Mouzan ◽

Asaad Assiri ◽

Ahmed Al Sarkhy ◽

Mona Alasmi ◽

Anjum Saeed ◽

...

Keyword(s):

Celiac Disease ◽

Beta Diversity ◽

Alpha Diversity ◽

Abundant Species ◽

Intestinal Microbiome ◽

Human Polyomavirus ◽

Fecal Samples ◽

Linear Discriminant ◽

Immune Mediated ◽

New Onset

Viruses are common components of the intestinal microbiome, modulating host bacterial metabolism and interacting with the immune system, with a possible role in the pathogenesis of immune-mediated diseases such as celiac disease (CeD). The objective of this study was to characterize the virome profile in children with new-onset CeD. We used metagenomic analysis of viral DNA in mucosal and fecal samples from children with CeD and controls and performed sequencing using the Nextera XT library preparation kit. Abundance log2 fold changes were calculated using differential expression and linear discriminant effect size. Shannon alpha and Bray–Curtis beta diversity were determined. A total of 40 children with CeD and 39 controls were included. We found viral dysbiosis in both fecal and mucosal samples. Examples of significantly more abundant species in fecal samples of children with CeD included Human polyomavirus 2, Enterobacteria phage mEpX1, and Enterobacteria phage mEpX2; whereas less abundant species included Lactococcus phages ul36 and Streptococcus phage Abc2. In mucosal samples however, no species were significantly associated with CeD. Shannon alpha diversity was not significantly different between CeD and non-CeD groups and Bray–Curtis beta diversity showed no significant separation between CeD and non-CeD samples in either mucosal or stool samples, whereas separation was clear in all samples. We identified significant viral dysbiosis in children with CeD, suggesting a potential role in the pathogenesis of CeD indicating the need for further studies.

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Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development

PeerJ ◽

10.7717/peerj.9003 ◽

2020 ◽

Vol 8 ◽

pp. e9003

Author(s):

Zhongwei Yin ◽

Keping Sun ◽

Aoqiang Li ◽

Deyi Sun ◽

Zhongle Li ◽

...

Keyword(s):

Gut Microbiota ◽

Beta Diversity ◽

Redundancy Analysis ◽

Transition Period ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Alpha And Beta Diversity ◽

Compositional Changes ◽

Gut Microbial Community ◽

Host Development

Background The gut microbiota is closely linked to host development, diet and health and is influenced by both the host and the environment. Although many studies have focused on the dynamics of the gut microbiota during development in captive animals, few studies have focused on the dynamics of the gut microbiota during development in wild animals, especially for the order Chiroptera. Methods In this study, we characterized the gut microbiota of the wild Asian particolored bat (Vespertilio sinensis) from 1 day to 6 weeks after birth. We explored the changes in their gut microbial community compositions, examined possible influencing factors, and predicted the feeding transition period. Results The gut microbiota changed during the development of V. sinensis. The alpha diversity of the bats’ gut microbiota gradually increased but did not change significantly from the 1st day to the 4th week after birth; however, the alpha diversity decreased significantly in week 5, then stabilized. The beta diversity differed slightly in weeks 4–6. In week 4, the fecal samples showed the highest diversity in bacterial community composition. Thus, we predicted that the potential feeding transition period for V. sinensis may occur during week 4. Redundancy analysis showed that age and body mass index significantly affected the compositional changes of the gut microbiota in Asian particolored bats. Conclusion The gut microbiota changed during the development of V. sinensis. We suggest that changes in the alpha and beta diversity during week 4 after birth indicate a potential feeding transition, highlighting the importance of diet in the gut microbiota during the development of V. sinensis.

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Fecal biomarkers of environmental enteric dysfunction and the gut microbiota of rural Malawian children: an observational study

10.1101/2021.01.19.21250144 ◽

2021 ◽

Author(s):

David Chaima ◽

Harry Pickering ◽

John D. Hart ◽

Sarah E. Burr ◽

Kenneth M. Maleta ◽

...

Keyword(s):

Gut Microbiota ◽

Low Income ◽

Inflammatory Responses ◽

Alpha Diversity ◽

List Type ◽

Fecal Samples ◽

Pyrimidine Nucleotide ◽

Neopterin Concentration ◽

Environmental Enteric Dysfunction ◽

Alpha 1 Antitrypsin

SummaryEnvironmental enteric dysfunction (EED) is a subclinical condition of the gut characterized by changes in morphology and function with underlying chronic inflammatory responses. This study characterized composition and diversity of the gut microbiota in rural Malawian children with and without signs of EED. Fecal samples were collected from children aged 1-59 months. Neopterin, myeloperoxidase and alpha-1 antitrypsin concentrations were quantified by ELISA and combined to form a composite EED score using principal component analysis. DNA was extracted from fecal samples and V4-16S rRNA sequencing was used to characterize the gut microbiota. The concentrations of all three biomarkers decreased with increasing age, which is consistent with other studies of children living in similar low-income settings. Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were the dominant phyla while Faecalibacterium and Bifidobacterium were the most prevalent genera. Increased alpha diversity was associated with a reduction in neopterin concentration. Microbiota composition was associated with the composite EED score. Increased abundance of Succinivibrio was associated with reduced composite EED scores.HighlightsIn Malawian children, fecal concentrations of myeloperoxidase, alpha-1 antitrypsin and neopterin decreased with ageA marginal negative association was found between alpha diversity of the gut microbiota and fecal neopterin concentrationA higher abundance of Succinivibrio was found in children with lower concentrations of biomarker of environmental enteric dysfunctionFatty acid biosynthesis, tetrapyrrole biosynthesis and pyrimidine nucleotide degradation pathways were associated with environmental enteric dysfunction biomarker score

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Prebiotic Effects of a Cranberry Beverage in a Randomized, Placebo-Controlled, Crossover Clinical Trial

Current Developments in Nutrition ◽

10.1093/cdn/nzab054_045 ◽

2021 ◽

Vol 5 (Supplement_2) ◽

pp. 1190-1190

Author(s):

Jingcheng Zhao ◽

Yunhui Qi ◽

Peng Liu ◽

Andrew Severin ◽

Maryam Sayadi ◽

...

Keyword(s):

Fatty Acid ◽

Gut Microbiota ◽

Beta Diversity ◽

Short Chain Fatty Acid ◽

Dietary Intervention ◽

Alpha Diversity ◽

Chain Fatty Acid ◽

Short Chain ◽

Controlled Study ◽

Rrna Gene

Abstract Objectives The objective was to evaluate the prebiotic effects of a milled whole cranberry beverage on modulating the gut microbiota in young adults. Methods Adults (n = 17; ages 18–42 y; BMI 30.5 ± 3.1 kg/m2) were enrolled in a 60-d, two-period, randomized, placebo-controlled, crossover clinical study. Throughout the study, participants were fed a standardized 10-d cycle menu on site. During each 20-d treatment period, participants consumed twice daily a whole cranberry or placebo beverage (240 mL per serving). Treatment periods were separated by an 11-wk washout period and preceded by 10-d run-in periods on the controlled study diet. Fecal samples were collected before and after the dietary intervention for bacterial compositional analysis and short-chain fatty acid analysis by LC-MS/MS. The V5-V6 region of the 16S rRNA gene in fecal DNA was amplified and sequenced. Taxonomy was assigned using the q2-feature-classifier in QIIME2 and matched against the Greengenes 13_8 database. Differential abundance was analyzed using ANCOM2 in R. Alpha-diversity was assessed using Faith's PD, Shannon diversity, and observed OTU richness generated by QIIME 2 and compared between treatments using Mann-Whitney U test. Beta-diversity was compared between treatments using PERMANOVA of the weighted and unweighted UniFrac distances between samples generated by QIIME 2. Results Coriobacteriaceae was significantly more abundant after participants consumed the cranberry as compared with the placebo beverage (ANCOM W > 0.7). The clinically-important pathogen Clostridium perfringens was present after consumption of the placebo beverage, but was a structural zero (not present) after consumption of the cranberry beverage. Alpha-diversity, beta-diversity, and fecal short-chain fatty acid concentrations did not differ between treatments. Conclusions Daily consumption of a whole cranberry beverage resulted in favorable change in the composition of the gut microbiota and thus showed prebiotic potential. Funding Sources Ocean Spray Cranberries, Inc.

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