Microbial composition associated with biliary stents in patients undergoing pancreatic resection for cancer

Malignant bile duct obstruction is typically treated by biliary stenting, which however increases the risk of bacterial infections. Here, we analyzed the microbial content of the biliary stents from 56 patients finding widespread microbial colonization. Seventeen of 36 prevalent stent species are common oral microbiome members, associate with disease conditions when present in the gut, and include dozens of biofilm- and antimicrobial resistance-related genes. This work provides an overview of the microbial communities populating the stents.

Draft genome sequence of a representative strain of the Catenibacterium genus isolated from human feces

A strain from a previously undescribed species belonging to the Catenibacterium genus was isolated from the stool of a healthy volunteer. The strain is strictly anaerobic, and the genome encodes a CRISPR-Cas system and genes related to trimethylamine production.

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice

Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.

Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population

The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns.

The person-to-person transmission landscape of the gut and oral microbiomes

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.

Abstract 3059: Microbiota mediated CHI3L1 expression as a novel candidate biomarker for breast cancer progression

Over the past decade, infectious agents, including bacteria, have come under scrutiny for contributing to almost 16% of all tumors. Indeed, emerging data report a microbial presence in many cancer types, with breast cancer accumulating the most diverse bacterial population. Pathogen defense mechanisms, such as CHI3L1, contribute to bacterial elimination; however, CHI3L1 is overexpressed in several cancer types and correlates with poor prognosis and shorter survival. However, the connection between intra-tumoral bacteria and CHI3L1 and how they contribute to cancer growth has not been fully characterized.To investigate if microbiota and CHI3L1 are connected, female BALB/c mice harboring 4T1-Luc cells were exposed to a broad-spectrum antibiotic mix to deplete the microbiota and to evaluate tumor growth and circulating CHI3L1 levels. 9 and 14 days after tumor inoculation, feces were collected and bacterial DNA isolated for 16S rRNA sequencing, and tumors were plated to identify intratumoral bacteria. To assess whether a specific bacterial strain could modulate CHI3L1 expression, we incubated 4T1 cells with supernatants from isolated bacteria, which contain metabolites and extracellular factors. Isolated bacteria that could upregulate CHI3L1 expression were then used to infect 4T1 cells prior to subcutaneous injection in the mammary fat pad of BALB/c mice to evaluate if bacterial infection changes tumor growth rate.In the 4T1 mouse breast cancer model, a broad-spectrum antibiotic treatment was able to: deplete host microbiota, abrogate tumor growth, and reduce CHI3L1 levels in the sera and in CD45+ immune infiltrating cells in tumor and colon. When 4T1 cells were exposed to bacterial supernatants in vitro, we observed that CHI3L1 was upregulated by a specific strain of E. coli. To simulate the effect of intra-tumoral microbiota, we infected 4T1 cells with either the isolated E. coli or S. aureus (which did not induce any CHI3L1 modulation in vitro) prior to subcutaneous injection. Strikingly, E. coli infection increased tumor progression with respect to the control S. aureus infection (p<0.01).Moreover, we observed an increase in CHI3L1 produced by tumor immune infiltrates in E. coli-infected 4T1, highlighting a key role for microbiota and CHI3L1 in tumor progression. Overall, our findings shed light on the important link between tumor associated bacteria and CHI3L1 in cancer progression. Identifying the mechanism of action through which microbiota and CHI3L1 influence cancer growth will open new possibilities for improved screening, prognosis, and survival for patients with breast cancer.

Citation Format: Alessandro Mauro Mozzarelli, Sara Carloni, Valentina Ferrrari, Silvia Giugliano, Luca Tiraboschi, Antonino Lo Cascio, Giulia Fornasa, Daniele Braga, Davide Golzato, Nicola Segata, Giuseppe Penna, Maria Rescigno. Microbiota mediated CHI3L1 expression as a novel candidate biomarker for breast cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3059.

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

BACKGROUND

Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored.

RESULTS

We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon.

CONCLUSIONS

We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria.