MICROBIOME

PUBLICATIONS

on microbial population

The Microbiome Research Hub is the place where experts from different scientific areas come together and collaborate. The most obvious proof for research success is represented by the (joint) publication of scientific results.

Below is the list of published work from our affiliated faculty and scientists. 

SELECTED ASPECTS OF THE HUMAN GUT MICROBIOTA

Ventura M, O'Toole PW, de Vos WM, van Sinderen D.

Abstract

The gut microbiota represents a highly complex assembly of microbes, which interact with each other and with their host. These interactions have various implications in terms of health and disease, and this multi-author review issue will address a number of selected aspects pertaining to gut microbiota research.

Cell Mol Life Sci. 2017 Oct 6​

Ventura M, O'Toole PW, de Vos WM and van Sinderen D. Selected aspects of the human gut microbiota. 2017, Cell Mol Life Sci.

BIFIDOBACTERIA AND THE INFANT GUT: AN EXAMPLE OF CO-EVOLUTION AND NATURAL SELECTION.

Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA, Mancabelli L, van Sinderen D, Ventura M.​

Abstract

Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.

Cell Mol Life Sci. 2017 Oct 5.​

Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA, Mancabelli L, van Sinderen D, Ventura M. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. 2017, Cell Mol Life Sci.

IDENTIFICATION OF UNIVERSAL GUT MICROBIAL BIOMARKERS OF COMMON HUMAN INTESTINAL DISEASES BY META-ANALYSIS

Mancabelli L, Milani C, Lugli GA, Turroni F, Cocconi D, van Sinderen D, Ventura M.​

Abstract

Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next Generation Sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although formulation of universal gutmicrobial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects (CTRL). Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.

FEMS Microbiol Ecol. 2017 Nov 8.​

Mancabelli, L., Milani, C., Lugli, G.A., Turroni, F., Cocconi, D., van Sinderen, D., and Ventura, M. Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis. 2017. FEMS Microbiology Ecology. 

GLYCAN UTILIZATION AND CROSS-FEEDING ACTIVITIES BY BIFOBACTERIA.

Turroni F, Milani C, Duranti S, Mahony J, van Sinderen D, Ventura M.​

Abstract

Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next Generation Sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although formulation of universal gut microbial biomarkers for such diseases   is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects (CTRL). Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.

Trends Microbiol. 2017 Oct 28​

Turroni, F., Milani, C., Duranti, S., Mahony, J., van Sinderen, D., and Ventura, M.. Glycan utilization and cross-feeding activities by bifidobacteria. 2017 Trends in Microbiology 

UNTANGLING THE CECAL MICROBIOTA OF FERAL CHICKENS BY CULTURMONIC AND METAGENOMIC ANALYSES.

Ferrario C, Alessandri G, Mancabelli L, Gering E, Mangifesta M, Milani C, Lugli GA, Viappiani A, Duranti S, Turroni F, Ossiprandi MC, Hiyashi R, Mackie R, van Sinderen D, Ventura M.​

Abstract

Bifidobacteria represent one of the first colonizers of the mammalian gut, where such colonization is facilitated by their saccharolytic capabilities. Genomic analyses of bifidobacteria have revealed intriguing genetic strategies employed by these bacteria to access a variety of dietary and host-produced glycans. Bifidobacterial genome evolution therefore represents a fascinating example of how their chromosomes were molded to contain a large number of genes involved in carbohydrate metabolism. One of the reasons as to why bifidobacteria are such dominant and prevalent members of the (early) microbiota is that they may access glycans in the gut through mutualistic cross-feeding or resource-sharing activities, which is indicative of 'social behavior' among bifidobacterial strains.

Environ Microbiol. 2017 Oct 2.​

Ferrario, C., Alessandri, G., Mancabelli, L., Gering, E., Mangifesta, M., Milani, C., Lugli, G.A., Viappiani, A., Duranti, S., Turroni, F., Ossiprandi, M.C., Hiyashi, R., Mackie, R., van Sinderen, D., and Ventura, M. 2017. Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses (in press) (IF: 6.24).

THE FIRST MICROBIAL COLONIZERS OF THE HUMANG GUT: COMPOSITION, ACTIVITIES AND HEALTH IMPLICATIONS OF THE INFANT GIT MICROBIOTA

Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M.​

Abstract

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this humansecretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult healthconditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbialplayers of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.

Microbiol Mol Biol Rev. 2017 Nov 8​

Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Delgado, S., Arboleya, S., Mancabelli, L., Lugli, G.A., Rodriguez, J.M., Bode, L., de Vos, W., Gueimonde, M., Margolles, A., van Sinderen, D., and Ventura, M. 2017. The first microbial colonizers of the human gut: composition, activities and health implications of the infant gut microbiota. Microbiology and Molecular Biology Reviews