Modulation of Gut Microbiota and Immune System by Probiotics, Pre-biotics, and Post-biotics

The human gastrointestinal tract harbours a complex microbial community, which interacts with the mucosal immune system closely. Gut microbiota plays a significant role in maintaining host health, which could supply various nutrients, regulate energy balance, modulate the immune response, and defence against pathogens. Therefore, maintaining a favourable equilibrium of gut microbiota through modulating bacteria composition, diversity, and their activity is beneficial to host health. Several studies have shown that probiotics and pre-biotics could directly and indirectly regulate microbiota and immune response. In addition, post-biotics, such as the bioactive metabolites, produced by gut microbiota, and/or cell-wall components released by probiotics, also have been shown to inhibit pathogen growth, maintain microbiota balance, and regulate an immune response. This review summarises the studies concerning the impact of probiotics, pre-biotics, and post-biotics on gut microbiota and immune systems and also describes the underlying mechanisms of beneficial effects of these substances. Finally, the future and challenges of probiotics, pre-biotics, and post-biotics are proposed.

Antibiotic treatment impaired growth of tobacco in vitro shoots is associated with oxidative injury and reduced microbiome diversity

Plant in vitro cultures initiated from surface-sterilized explants often harbor complex microbial community. Antibiotics are commonly used to decontaminate plant tissue culture or during genetic transformation, however, the effect of antibiotic treatment on the diversity of indigenous microbial population and consequences for performance of the tissue culture are not completely understood. Therefore, the aim of this study was to assess the effect of antibiotic treatment on the growth and stress level of tobacco (Nicotiana tabacum L.) in vitro shoots as well as the composition of plant-associated microbiome. The study revealed that shoot cultivation on medium supplemented with 250 mg L−1 timentin resulted in 29 ± 4% reduced biomass accumulation and 1.2–1.6 fold higher level of oxidative stress injury compared to control. Moreover, the growth properties of shoots were only partially restored after transfer to medium without antibiotic. Shoot microbiome analysis using multi-variable region-based 16S rRNA sequencing revealed abundant microbial community in the control tobacco shoots, including bacteria from 59 families, however, it was largely dominated by Mycobacteriaceae. The antibiotic treatment resulted in a decline of species richness (the number of families was reduced 4.5-fold) and increased domination by the Mycobacteriaceae family. The results imply that the diversity of plant-associated microbiome might represent a significant factor contributing to the efficient propagation of in vitro tissue culture.

Assessing long-read sequencing with Nanopore R9, R10, and PacBio CCS to obtain high-quality metagenome assembled genomes from complex microbial communities

Short-read DNA sequencing has led to a massive growth of genome databases but mainly with highly fragmented metagenome assembled genomes from environmental systems. The fragmentation is a result of closely related species, strains, and genome repeats that cannot be resolved with short reads. To confidently explore the functional potential of a microbial community, high-quality reference genomes are needed. In this study, we evaluated the use of different combinations of short (Illumina) and long-read technologies (Nanopore R9.4, R10.3, and PacBio CCS) for recovering high-quality metagenome assembled genomes (HQ MAGs) from a complex microbial community (anaerobic digester). Depending on the sequencing approach, 33 to 86 HQ MAGs (encompassing up to 34 % of the assembly and 49 % of the reads) were recovered using long reads, with Nanopore R9 featuring the lowest sequencing costs per HQ MAG recovered. PacBio CCS was also found to be an effective platform for genome-centric metagenomics (74 HQ MAGs) and produced HQ MAGs with the lowest fragmentation (median of 9 contigs) as a stand-alone technology. Using PacBio CCS MAGs as reference, we show that, although a high number of high-quality MAGs can be generated using Nanopore R9, systematic indel errors are still present, which can lead to truncated gene calling. However, polishing the Nanopore MAGs with short-read Illumina data, enabled recovery of MAGs with similar quality as MAGs from PacBio CCS.

A Common Pathway for Activation of Host-Targeting and Bacteria-Targeting Toxins in Human Intestinal Bacteria

The human intestine harbors a highly complex microbial community; interpersonal variation in this community can impact pathogen susceptibility, metabolism, and other aspects of health. Here, we identified and characterized a commensal-targeting antibacterial protein encoded in the gut microbiome.

A qPCR-based method for rapid quantification of six intestinal homeostasis-relevant bacterial genera in feces

Aim: Developing efficient methods for monitoring the complex microbial community to rapidly assess the health status. Materials & methods: The qPCR-based method was developed, verified and in situ applied in fecal samples. Results: Six primer pairs with high specificity were designed to perform qPCR assays under a unified reaction condition within 2.5 h. The limits of detection, amplification efficiency and feasibility of the qPCR-based method established here were verified. In situ application of 18 fecal samples showed that the amounts of Bacteroides, Streptococcus and Bifidobacterium in colorectal cancer patient feces were obviously lower than those of healthy volunteers. Conclusion: This qPCR-based method was a reliable tool for rapid quantification of the six intestinal homeostasis relevant bacterial genera in feces.

Alphavirus and flavivirus infectivity is disrupted by components of the bacterial cell wall

The impact of the host microbiome on arbovirus infections is currently not clearly understood. Arboviruses are viruses transmitted through the bites of infected arthropods, predominantly mosquitoes or ticks. The first site of arbovirus inoculation is the biting site in the host skin, which is colonized by a complex microbial community that could possibly influence arbovirus infection. We demonstrated that pre-incubation of arboviruses with certain components of the bacterial cell wall, including lipopolysaccharides (LPS) of some Gram-negative bacteria and lipoteichoic acids or peptidoglycan of certain Gram-positive bacteria, significantly reduced arbovirus infectivity in vitro. This inhibitory effect was observed for arboviruses of different virus families, including chikungunya virus of the Alphavirus genus and Zika virus of the Flavivirus genus, showing that this is a broad phenomenon. A modest inhibitory effect was observed following incubation with a panel of heat-inactivated bacteria, including bacteria residing on the skin. No viral inhibition was observed after pre-incubation of cells with LPS. Furthermore, a virucidal effect of LPS on viral particles was noticed by electron microscopy. Therefore, the main inhibitory mechanism seems to be due to a direct effect on the virus particles. Together, these results suggest that bacteria are able to decrease the infectivity of alphaviruses and flaviviruses.

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Background The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Conclusions Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis

Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with ≥80% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.

Deconstructing then Priming Gut Microbiota Resilience

The human intestinal microbiota represents a complex microbial community that plays an essential role in the maintenance of host health. Over the last decade, metagenomic and metabolomic analyses have revealed the influence of intestinal microbial diversity and composition on a range of biological functions in the host. While overall taxonomic composition of the intestinal microbiome is informative, changes in spatial dynamics within the community also have profound biological significance as microbial functions are influenced by neighbouring community members and the microenvironment. Critical gaps remain in our understanding of microbiota structure, co-dependences, resilience and response to antimicrobial agents. In this review, we discuss alternative strategies to deconstruct the microbiome to yield better designed and more clinically effective therapies.