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

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.

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Supplementation of a Lacto-fermented Rapeseed-seaweed Blend Promotes Gut Microbial- and Gut Immune-Modulation in Weaner Piglets

10.21203/rs.3.rs-142255/v1 ◽

2021 ◽

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 ◽

Gut Health ◽

Brown Macroalgae ◽

Final Body Weight ◽

Blood Concentrations

Abstract BackgroundThe 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.ResultsThis study assessed whether rapeseed meal added two brown macroalgae species (Saccharina latissima and Ascophylum nodosum) and fermented using lactic acid bacteria (FRS) could improve weaner piglet performance and gut health. From day 28 of life to day 85, the weaned piglets were fed one of three different feeding regimens (n = 230 each) with inclusion of 0%, 2.5% and 5% FRS. The piglets fed with 2.5% FRS manifested superior phenotype with alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier and numerical increase of final body weight. The colon microbiota composition was determined using the 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 consistence between the detected bacteria. Both sequencing strategies indicated that inclusion of FRS reshaped the colon microbiome of weaner piglets with increased Shannon diversity. Prevotella stercorea was verified by both technologies to be more abundant in the FRS piglets, and its abundance was positively correlated with colon mucosa thickness but negatively correlated with blood concentrations of leucocytes and IgG.ConclusionsFRS supplementation improved the gut health of weaner piglets, and reshaped the gut microbiota composition. Increasing the dietary inclusion of FRS from 2.5% to 5% did not lead to further improvements.

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

10.1101/2020.09.22.308106 ◽

2020 ◽

Author(s):

Yan Hui ◽

Paulina Tamez-Hidalgo ◽

Tomasz Cieplak ◽

Gizaw Dabessa Satessa ◽

Witold Kot ◽

...

Keyword(s):

Basal Diet ◽

Amplicon Sequencing ◽

Saccharina Latissima ◽

Blood Levels ◽

Rrna Gene ◽

Microbiota Composition ◽

Colon Mucosa ◽

Gut Health ◽

Microbial Composition ◽

Final Body Weight

AbstractThe direct use of medical zinc oxide (ZnO) in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders. This study assessed whether rapeseed meal added two brown macroalagae species (Saccharina latissima and Ascophylum nodosum) and fermented using lactic acid bacteria (FRS) could improve piglet performance and gut health. The weaned piglets were fed one of three different feeding regimens (n = 230 each): basal diet, 2.5% and 5% FRS from day 28 of life to day 85. The piglets fed with 2.5% FRS presented superior phenotype with alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier as well as numerically improvements of final body weight. Colon microbiota composition was determined using amplicon sequencing of the V3 and V1 – V8 region of the 16S rRNA gene using Illumina Nextseq and Oxford Nanopore MinION sequencing, respectively. The two amplicon sequencing strategies showed high consistence between the detected bacteria. Both sequencing technologies showed that the FRS fed piglets had a distinctly different microbial composition relative to the basal diet. Compared with piglets fed the basal diet, Prevotella stercorea was verified by both technologies to be more abundant in the FRS piglets, and positively correlated with colon mucosa thickness and negatively correlated with blood levels of leucocytes and IgG. In conclusion, FRS supplementation improved gut health of weaner piglets, and altered their gut microbiota composition. Increasing the dietary inclusion of FRS from 2.5% to 5% did not cause further improvements.

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

Tropical Animal Health and Production ◽

10.1007/s11250-020-02535-9 ◽

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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Comparative Analysis of Fecal Microbiota Composition Between Rheumatoid Arthritis and Osteoarthritis Patients

Genes ◽

10.3390/genes10100748 ◽

2019 ◽

Vol 10 (10) ◽

pp. 748 ◽

Cited By ~ 5

Author(s):

Jin-Young Lee ◽

Mohamed Mannaa ◽

Yunkyung Kim ◽

Jehun Kim ◽

Geun-Tae Kim ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Gut Microbiota ◽

Gut Microbiome ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Microbiota Composition ◽

Stool Samples ◽

Gut Microbiota Composition

The aim of this study was to investigate differences between the gut microbiota composition in patients with rheumatoid arthritis (RA) and those with osteoarthritis (OA). Stool samples from nine RA patients and nine OA patients were collected, and DNA was extracted. The gut microbiome was assessed using 16S rRNA gene amplicon sequencing. The structures and differences in the gut microbiome between RA and OA were analyzed. The analysis of diversity revealed no differences in the complexity of samples. The RA group had a lower Bacteroidetes: Firmicutes ratio than did the OA group. Lactobacilli and Prevotella, particularly Prevotella copri, were more abundant in the RA than in the OA group, although these differences were not statistically significant. The relative abundance of Bacteroides and Bifidobacterium was lower in the RA group. At the species level, the abundance of certain bacterial species was significantly lower in the RA group, such as Fusicatenibacter saccharivorans, Dialister invisus, Clostridium leptum, Ruthenibacterium lactatiformans, Anaerotruncus colihominis, Bacteroides faecichinchillae, Harryflintia acetispora, Bacteroides acidifaciens, and Christensenella minuta. The microbial properties of the gut differed between RA and OA patients, and the RA dysbiosis revealed results similar to those of other autoimmune diseases, suggesting that a specific gut microbiota pattern is related to autoimmunity.

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Higher fiber complementary food alters Fecal microbiota composition and normalizes stool form in Malawian children: A randomized trial

African Journal of Food, Agriculture, Nutrition and Development ◽

10.18697/ajfand.99.20200 ◽

2021 ◽

Vol 21 (04) ◽

pp. 17854-17875

Author(s):

Edda Lungu ◽

◽

J Auger ◽

A Piano ◽

WJ Dahl ◽

...

Keyword(s):

Dietary Intake ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Stool Frequency ◽

Sub Saharan Africa ◽

Rrna Gene ◽

Microbiota Composition ◽

Linear Discriminant ◽

Stool Form

Dietary fiber favorably modulates gut microbiota and may be protective against diarrhea in sub-Saharan Africa where rates in infants and young children are high. Soybean hull is high in fiber and accessible in rural Africa; however, its use in complementary feeding has not been evaluated. The objective of this study was to determine the acceptability and feasibility of a soybean, soy hull fiber, and maize (SFM) blend food; the primary outcome was compliance to the feeding protocol. Secondary outcomes were stool form and frequency, fecal microbiota composition, growth and dietary intake. In a parallel, single-blind study, children 6-36 months of age from the Lilongwe district of Malawi were randomized to receive daily SFM (n=69) or maize only(n=10) porridge(phala) for 6 months. Anthropometrics were measured monthly, and compliance, stool frequency,and stool form, weekly. At baseline, 3-month,and 6-month (study end) time points, dietary intake (24-h recall) was assessed,and fecal samples were collected. Fecal DNA was analyzed by Real-Time polymerase chain reaction (PCR) for microbes of interest and 16S rRNA gene amplicon sequencing. Mothers accessed the acceptability and feasibility of the study foods at study end. Mothers reported excellent compliance to feeding the SFM porridge, rated it more acceptable than maize,and noted improved appetite, weight, and stool consistency of their children. Stool frequency at baseline (2±1 stools/d) was unchanged with intervention; however, there were significantly fewer diarrhea-type stools reported during study months 4-6 vs.1-3 for the SFM group, whereas no improvement was seen for the maize group. At study end, the fecal abundance ofAkkermansia muciniphila was enriched in children receiving the SFM, compared to maize (p<0.05), and a trend for increased Faecalibacterium prausnitzii (p=0.07) was seen. A comparison of fecal microbiota composition using linear discriminant analysis effect size (LEfSe)showed notable differences in numerous taxa in the SFM group compared to baseline, whereas the maize comparator exhibited fewer changes. Fiber intake was higher for the SFMgroup, compared to maize at 6 months (13.7±3.8 vs. 8.4±4.5 g/day, p<0.01). Weight-for-height and BMI-for-age Z-scores were significantly higher for the SFM group. In young Malawian children, feeding a blend of soybean, soy hulls and maize reduced diarrhea-type stools and increased the abundance of Akkermansia muciniphila, a bacterial species involved in maintaining intestinal health, and thus may provide a feasible means of improving wellness in children in resource-poor settings through the modulation of microbiota composition.

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Trikafta therapy alters the CF lung mucus metabolome reshaping microbiome niche space

10.1101/2021.06.02.21257731 ◽

2021 ◽

Author(s):

Lauren Sosinski ◽

Christian Martin-Hernandez ◽

Kerri A Neugebauer ◽

Lydia-Ann J Ghuneim ◽

Douglas V Guzior ◽

...

Keyword(s):

Drug Effects ◽

Amplicon Sequencing ◽

Kynurenine Pathway ◽

Rrna Gene ◽

Structural Modifications ◽

Lung Microbiome ◽

Fda Approval ◽

Significant Difference ◽

Before And After ◽

Log Ratio

Novel small molecule therapies for cystic fibrosis (CF) are showing promising efficacy and becoming more widely available since recent FDA approval. The newest of these is a triple therapy of Elexacaftor-Tezacaftor-Ivacaftor (ETI). Little is known about how these drugs will affect polymicrobial lung infections, which are the leading cause of morbidity and mortality among people with CF (pwCF). We analyzed the sputum microbiome and metabolome from pwCF (n=24) before and after TKT therapy using 16S rRNA gene amplicon sequencing and untargeted metabolomics. The lung microbiome diversity, particularly its evenness, was increased (p = 0.044) and the microbiome profiles were different between individuals before and after therapy (PERMANOVA F=1.92, p=0.044). Despite these changes, the microbiomes were more similar within an individual than across the sampled population. There were no specific microbial taxa that were different in abundance before and after therapy, but collectively, the log-ratio of anaerobes to pathogens significantly decreased. The sputum metabolome also showed changes due to TKT. Beta-diversity increased after therapy (PERMANOVA F=4.22, p=0.022) and was characterized by greater variation across subjects while on treatment. This significant difference in the metabolome was driven by a decrease in peptides, amino acids, and metabolites from the kynurenine pathway. Metabolism of the three small molecules that make up TKT was extensive, including previously uncharacterized structural modifications. This study shows that TKT therapy affects both the microbiome and metabolome of airway mucus. This effect was stronger on sputum biochemistry, which may reflect changing niche spaces for microbial residency in lung mucus as the drug effects take hold, which then leads to changing microbiology.

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Sex-Based Diverse Plaque Microbiota in Children with Severe Caries

Journal of Dental Research ◽

10.1177/0022034520908595 ◽

2020 ◽

Vol 99 (6) ◽

pp. 703-712 ◽

Cited By ~ 3

Author(s):

V.C. de Jesus ◽

R. Shikder ◽

D. Oryniak ◽

K. Mann ◽

A. Alamri ◽

...

Keyword(s):

Young Children ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Fungal Species ◽

Assessment Tools ◽

Rrna Gene ◽

Male And Female ◽

Significant Difference ◽

Female Children ◽

Related Quality

Severe early childhood caries (S-ECC) is a multifactorial disease that can lead to suffering and reduced oral health–related quality of life in young children. The bacterial and fungal composition of dental plaque and how children’s sex is associated with S-ECC are largely unknown. In this study, V4-16S rRNA and ITS1 rRNA gene amplicon sequencing was used to compare the plaque bacteriome and mycobiome of children <72 mo of age: 40 with S-ECC (15 males, 25 females) and 40 caries-free (19 males, 21 females). Health- and nutrition-related questionnaire data were also investigated. This study aimed to analyze potential sex-based differences in the supragingival plaque microbiota of young children with S-ECC and those caries-free. Behavioral and nutritional habit differences were observed between children with S-ECC and those caries-free and between male and female children. Overall, higher levels of Veillonella dispar, Streptococcus mutans, and other bacterial species were found in the S-ECC group as compared with caries-free controls ( P < 0.05). A significant difference in the abundance of Neisseria was observed between males and females with S-ECC ( P < .05). Fungal taxonomic analysis showed significantly higher levels of Candida dubliniensis in the plaque of children with S-ECC as compared with those caries-free ( P < 0.05), but no differences were observed with Candida albicans ( P > 0.05). Significant differences in the relative abundance of Mycosphaerella, Cyberlindnera, and Trichosporon fungal species were also observed between the caries-free and S-ECC groups ( P < 0.05). Machine learning analysis revealed the most important bacterial and fungal species for classifying S-ECC versus caries-free. Different patterns of crosstalk between microbial species were observed between male and female children. Our work demonstrates that plaque microbiota and sex may be important determinants for S-ECC and could be factors to consider for inclusion in caries risk assessment tools.

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Adults with Prader–Willi syndrome exhibit a unique microbiota profile

BMC Research Notes ◽

10.1186/s13104-021-05470-6 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Wendy J. Dahl ◽

Jérémie Auger ◽

Zainab Alyousif ◽

Jennifer L. Miller ◽

Thomas A. Tompkins

Keyword(s):

Adult Population ◽

Geographical Location ◽

Gastrointestinal Transit ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Machine Learning Algorithms ◽

Rrna Gene ◽

Prader Willi Syndrome ◽

Microbiota Composition ◽

Gastrointestinal Transit Time

Abstract Objective Adults with Prader–Willi syndrome (PWS) require less energy intake to maintain body weight than the general adult population. This, combined with their altered gastrointestinal transit time, may impact microbiota composition. The aim of the study was to determine if the fecal microbiota composition of adults with PWS differed from non-affected adults. Using usual diet/non-interventional samples, fecal microbiota composition was analyzed using 16S rRNA gene amplicon sequencing and data from adults with PWS were merged with four other adult cohorts that differed by geographical location and age. QIIME 2™ sample-classifier, machine learning algorithms were used to cross-train the samples and predict from which dataset the taxonomic profiles belong. Taxa that most distinguished between all datasets were extracted and a visual inspection of the R library PiratePlots was performed to select the taxa that differed in abundance specific to PWS. Results Fecal microbiota composition of adults with PWS showed low Blautia and enhanced RF39 (phyla Tenericutes), Ruminococcaceae, Alistipes, Erysipelotrichacaea, Parabacteriodes and Odoribacter. Higher abundance of Tenericutes, in particular, may be a signature characteristic of the PWS microbiota although its relationship, if any, to metabolic health is not yet known.

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Exploring the resident gut microbiota of stranded odontocetes: high similarities between two dolphin species Tursiops truncatus and Stenella coeruleoalba

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315420000983 ◽

2020 ◽

Vol 100 (7) ◽

pp. 1181-1188

Author(s):

Khaled F. A. Abdelrhman ◽

Alice Ciofini ◽

Giovanni Bacci ◽

Cecilia Mancusi ◽

Alessio Mengoni ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Communities ◽

Tursiops Truncatus ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Microbiota Composition ◽

Cetacean Species ◽

Stenella Coeruleoalba ◽

Interspecific Differences ◽

Gut Microbiota Composition

AbstractThe evaluation of symbiotic microbial communities occurring in the intestinal tract of animals has received great interest in recent years. However, little is known about gut microbial communities in cetaceans, despite their relevance in the ecology of marine communities. Here, we report an investigation using 16S rRNA gene amplicon sequencing of the resident gut microbiota of the two cetacean species Stenella coeruleoalba and Tursiops truncatus by sampling intestinal mucosa from specimens retrieved stranded along the Tyrrhenian coast of Tuscany (Italy). We found an abundance of members from Clostridiaceae and Fusobacteriaceae, which in total accounted for more than 50% of reads, in agreement with gut microbiota composition of other carnivorous mammals. Probably due to the limited number of samples available, sex, preservation status and also species, did not correlate with overall differences in the microbiota. Indeed, a high similarity of the taxonomic (family-level) composition between the gut microbiota of the two species was found. However, Pedobacter spp. was found abundant in amplicon sequencing libraries from S. coeruleoalba, while clostridia were more abundant from T. truncatus samples. Our results shed some light on the gut microbiota composition of two dolphin (S. coeruleoalba and T. truncatus) species, with specimens collected in the wild. Studies with a larger number of individuals are now needed to confirm these first results and evaluate the interspecific differences in relation to sex and age.

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Caecal Microbiota Composition of Experimental Laying Hens Differs According to Genetic Line and Vaccination to IBV

10.21203/rs.3.rs-177864/v1 ◽

2021 ◽

Author(s):

Marion Borey ◽

Bertrand Bed'Hom ◽

Nicolas Bruneau ◽

Jordi Estellé ◽

Frederik Larsen ◽

...

Keyword(s):

T Cells ◽

Gut Microbiota ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Microbiota Composition ◽

Genetic Line ◽

Vaccine Response ◽

Main Components ◽

Main Association ◽

Caecal Microbiota

Abstract BackgroundInteractions between the gut microbiota and the immune system may be involved in the vaccine response. In the present study, we studied the correlations between caecal microbiota composition and the immune response in six experimental laying hen lines harboring different haplotypes at the Major Histocompatibility complex (MHC), 7 weeks after their first vaccination against the infectious bronchitis virus (IBV). Two lines were previously considered as high responders (HR) to IBV vaccination and two other ones as low responders (LR). We explored to what extent the gut microbiota could be related to this variability through the characterization of caecal bacterial communities with a 16S rRNA gene amplicon sequencing approach, one week after an IBV infectious challenge. ResultsWe observed significant effects of both the vaccination and the genetic line on the microbiota, with lower bacterial richness in vaccinated chickens, especially in the Ruminococcaceae family. We also observed dissimilar caecal communities among the different MHC lines, and among the vaccinated and non-vaccinated animals. The effect of vaccination was similar in all the lines, with a reduced abundance of OTUs from the Ruminococcacea UCG-014 and Faecalibacterium genera, and an increased abundance of OTUs from the Eisenbergiella genus. The main association between the microbiota and the immune phenotypes implied TCRϒδ expression on TCRϒδ+ T cells, which especially shared negative associations with OTUs from the Escherichia-Shigella genus. Finally, opposing the HR and LR groups, we identified 3 OTUs more abundant in the HR group, from the Tyzzeralla family, the Angelakisella genus, and to a lower extent the Flavonifractor family. Conversely, an OTU from the CAG-352 genus was more abundant in the LR group. ConclusionsWe assessed that the caecal microbiota composition is associated with the IBV vaccine response in laying chickens, and that TCRϒδ expression on TCRϒδ+ T cells appears as one of the main components potentially involved in this interaction.

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