scholarly journals Effect of the Degree of Polymerization of Fructans on Ex Vivo Fermented Human Gut Microbiome

Nutrients ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1293 ◽  
Author(s):  
Erola Astó ◽  
Iago Méndez ◽  
Maria Rodríguez-Prado ◽  
Jordi Cuñé ◽  
Jordi Espadaler ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Alpha Diversity ◽  
Degree Of Polymerization ◽  
Metagenomic Sequencing ◽  
Beneficial Bacteria ◽  
Human Gut ◽  
Gastrointestinal Health ◽  
Healthy Donors ◽  
Acidification Activity ◽  
Other Regarding

Prebiotic supplements are used to promote gastrointestinal health by stimulating beneficial bacteria. The aim of this study was to compare the potential prebiotic effects of fructans with increasing degrees of polymerization, namely fructooligosaccharides (FOS) and inulins with a low and high polymerization degree (LPDI and HPDI, respectively), using an ex vivo fermentation system to simulate the colonic environment. The system was inoculated with pooled feces from three healthy donors with the same baseline enterotype. Changes in microbiota composition were measured by 16S metagenomic sequencing after 2, 7, and 14 days of fermentation, and acid production was measured throughout the experiment. Alpha-diversity decreased upon inoculation of the ex vivo fermentation under all treatments. Composition changed significantly across both treatments and time (ANOSIM p < 0.005 for both factors). HPDI and LPDI seemed to be similar to each other regarding composition and acidification activity, but different from the control and FOS. FOS differed from the control in terms of composition but not acidification. HDPI restored alpha-diversity on day 14 as compared to the control (Bonferroni p < 0.05). In conclusion, the prebiotic activity of fructans appears to depend on the degree of polymerization, with LPDI and especially HPDI having a greater effect than FOS.

scholarly journals Fructans with Varying Degree of Polymerization Enhance the Selective Growth of Bifidobacterium animalis subsp. lactis BB-12 in the Human Gut Microbiome In Vitro

2021 ◽  
Vol 11 (2) ◽  
pp. 598
Author(s):  
Pieter Van den Abbeele ◽  
Cindy Duysburgh ◽  
Jonas Ghyselinck ◽  
Shellen Goltz ◽  
Yulia Berezhnaya ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Lactate Production ◽  
Degree Of Polymerization ◽  
Human Gut ◽  
Short Term ◽  
Gastrointestinal Health ◽  
Bifidobacterium Animalis ◽  
Low Degree ◽  
Butyrate Production

Synbiotics aim to improve gastrointestinal health by combining pre- and probiotics. This study evaluated combinations of Bifidobacterium animalis subsp. lactis BB-12 with seven fructans: oligofructoses (OF1-OF2; low degree of polymerization (DP)), inulins (IN1-IN2-IN3; high DP) and OF/IN mixtures (OF/IN1-OF/IN2). During monoculture incubations, all fructans were fermented by BB-12 as followed from increased BB-12 numbers and increased acetate and lactate concentrations, with most pronounced fermentation for low DP fructans (OF1-OF2). Further, short-term colonic incubations for three human donors revealed that also in presence of a complex microbiota, all fructans (particularly OF1) consistently selectively enhanced the growth of BB-12. While each fructan as such already increased Bifidobacteriaceae numbers with 0.94–1.26 log(cells/mL), BB-12 co-supplementation additionally increased Bifidobacteriaceae with 0.17–0.46 log(cells/mL). Further, when co-supplemented with fructans, BB-12 decreased Enterobacteriaceae numbers (significant except for IN1-IN3). At metabolic level, all fructans decreased pH due to increased acetate and lactate production, while OF/IN2-IN1-IN2-IN3 also stimulated propionate and butyrate production. BB-12 co-supplementation further increased propionate and butyrate for OF/IN2-IN3 and IN1-IN2, respectively. Overall, combinations of BB-12 with fructans are promising synbiotic concepts, likely due to intracellular consumption of low DP-fructans by BB-12 (either present in starting product or released upon fermentation by indigenous microbes), thereby enhancing effects of the co-administered fructan.

scholarly journals Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut

2018 ◽  
Author(s):  
Emma Guerin ◽  
Andrey Shkoporov ◽  
Stephen R. Stockdale ◽  
Adam G. Clooney ◽  
Feargal J. Ryan ◽  
...  
Keyword(s):  
Classification Scheme ◽  
Ex Vivo ◽  
Human Microbiome ◽  
Biological Entity ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Taxonomic Analysis ◽  
Faecal Samples ◽  
Phage Capsid

AbstractCrAssphage is yet to be cultured even though it represents the most abundant virus in the gut microbiota of humans. Recently, sequence based classification was performed on distantly related crAss-like phages from multiple environments, leading to the proposal of a familial level taxonomic group [Yutin N, et al. (2018) Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat Microbiol 3(1):38–46]. Here, we assembled the metagenomic sequencing reads from 702 human faecal virome/phageome samples and obtained 98 complete circular crAss-like phage genomes and 145 contigs ≥70kb. In silico comparative genomics and taxonomic analysis was performed, resulting in a classification scheme of crAss-like phages from human faecal microbiomes into 4 candidate subfamilies composed of 10 candidate genera. Moreover, laboratory analysis was performed on faecal samples from an individual harbouring 7 distinct crAss-like phages. We achieved propagation of crAss-like phages in ex vivo human faecal fermentations and visualised Podoviridae virions by electron microscopy. Furthermore, detection of a crAss-like phage capsid protein could be linked to metagenomic sequencing data confirming crAss-like phage structural annotations.SignificanceCrAssphage is the most abundant biological entity in the human gut, but it remains uncultured in the laboratory and its host(s) is unknown. CrAssphage was not identified in metagenomic studies for many years as its sequence is so different from anything present in databases. To this day, it can only be detected from sequences assembled from metagenomics or viromic datasets (crAss – cross Assembly). In this study, we identified 243 new crAss-like phages from human faecal metagenomic studies. Taxonomic analysis of these crAss-like phages highlighted their extensive diversity within the human microbiome. We also present the first propagation of crAssphage in faecal fermentations and provide the first electron micrographs of this extraordinary bacteriophage.

scholarly journals Healthy Protection Of Bergamot Is Linked To The Modulation Of Microbiota

2020 ◽  
Author(s):  
Antonella Riva ◽  
Valeria Longo ◽  
Davide Berlanda ◽  
Pietro Allegrini ◽  
Giulia Masetti ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Delivery System ◽  
Weight Control ◽  
Cardiovascular Health ◽  
Ex Vivo ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Potential Applications

Abstract Background: The present study aimed to evaluate the effects of a new food-grade bioavailable delivery system of bergamot on human gut microbiota, in order to demonstrate the potential correlation of microbiota modulation in cardiovascular health.The identification of human gut microbiota modification was performed after ex-vivo incubation with bergamot phytosome (Vazguard™) of individual faecal slurries from healthy women (45–53 years) as follows: after incubation at 37°C in anaerobic condition, DNA was extracted and a 16S Metagenomic Sequencing Analysis performed. Results: Twenty-five different phyla were identified, among which 4 were modulated: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria. The decreased Firmicutes/Bacteroidetes ratio and the increase of Proteobacteria were observed indicating a positive modulation of microbiota possibly linked to cardiovascular health. 418 different genera were also identified, among which several of them were mildly modulated.Conclusions: For the first time, a gut microbiome modulation was associated to the new delivery system of bergamot phytosome, supporting its clinical efficacy for cardiovascular health. New potential applications in weight control and gastrointestinal benefits were suggested.

scholarly journals Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Shi Huang ◽  
Shuaiming Jiang ◽  
Dongxue Huo ◽  
Celeste Allaband ◽  
Mehrbod Estaki ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Genetic Stability ◽  
Ex Vivo ◽  
Adverse Outcomes ◽  
Metagenomic Sequencing ◽  
Human Gut ◽  
Carbohydrate Utilization ◽  
Evolutionary Changes

Abstract Background Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods. Results We combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10–70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice. Conclusions Collectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans.

scholarly journals Novel strain-level resolution of Crohn’s disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing

2021 ◽  
Author(s):  
J. J. Teh ◽  
E. M. Berendsen ◽  
E. C. Hoedt ◽  
S. Kang ◽  
J. Zhang ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Ex Vivo ◽  
Taxonomic Composition ◽  
Strain Level ◽  
Patient Specific ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Functional Characterisation ◽  
Bacterial Lineages

AbstractThe mucosa-associated microbiota is widely recognized as a potential trigger for Crohn’s disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative Crohn’s disease patients. The 16 S rRNA gene amplicon profiles showed these cultures provide a representative and holistic representation of the mucosa-associated microbiota, and MC-MGS produced both high quality metagenome-assembled genomes of recovered novel bacterial lineages. The MC-MGS approach also produced a strain-level resolution of key Enterobacteriacea and their associated virulence factors and revealed that urease activity underpins a key and diverse metabolic guild in these communities, which was confirmed by culture-based studies with axenic cultures. Collectively, these findings using MC-MGS show that the Crohn’s disease mucosa-associated microbiota possesses taxonomic and functional attributes that are highly individualistic, borne at least in part by novel bacterial lineages not readily isolated or characterised from stool samples using current sequencing approaches.

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

Rapamycin enriches for CD4+ CD25+ CD27+ Foxp3+ regulatory T cells in ex vivo-expanded CD25-enriched products from healthy donors and patients with multiple sclerosis

Cytotherapy ◽  
2007 ◽  
Vol 9 (2) ◽  
pp. 144-157 ◽  
Author(s):  
Ca Keever-Taylor ◽  
Mb Browning ◽  
Bd Johnson ◽  
Rl Truitt ◽  
Cn Bredeson ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
T Cells ◽  
Regulatory T Cells ◽  
Ex Vivo ◽  
Healthy Donors

scholarly journals Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2093
Author(s):  
Shen-Yuan Hsieh ◽  
Mohammad A. Tariq ◽  
Andrea Telatin ◽  
Rebecca Ansorge ◽  
Evelien M. Adriaenssens ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
Diversity Indices ◽  
P Value ◽  
Library Preparation ◽  
High Genetic Diversity ◽  
Sequencing Platform ◽  
Viral Genomes ◽  
Healthy Donors ◽  
Faecal Samples ◽  
Sequencing Platforms

The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as “viral dark matter”. However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating “rare” members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.

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