Shrinkage of the human core microbiome and a proposal for launching microbiome biobanks

Impact of cryoprotective agents on human gut microbes and in vitro stabilized artificial gut microbiota communities

The availability of microbial biobanks for the storage of individual gut microbiota members or their derived and artificially assembled consortia has become fundamental for in vitro investigation of the molecular mechanisms behind microbe-microbe and/or microbe-host interactions. However, to preserve bacterial viability, adequate storage and processing technologies are required. In this study, the effects on cell viability of seven different combinations of cryoprotective agents were evaluated by flow cytometry for 53 bacterial species representing key members of the human gut microbiota after one and 3 months of cryopreservation at -80°C. The obtained results highlighted that no universal cryoprotectant was identified capable of guaranteeing effective recovery of intact cells after cryopreservation for all tested bacteria. However, the presence of inulin or skimmed milk provided high levels of viability protection during cryoexposure. These results were further corroborated by cryopreserving 10 artificial gut microbiota produced through in vitro continuous fermentation system technology. Indeed, in this case, the inclusion of inulin or skimmed milk resulted in a high recovery of viable cells, while also allowing consistent and reliable preservation of the artificial gut microbiota biodiversity. Overall, these results suggest that, although the efficacy of various cryoprotective agents is species-specific, some cryoprotectants based on glycerol and the addition of inulin or skimmed milk are preferable to retain viability and biodiversity for both single bacterial species and artificial gut microbiota.

Native microbiomes in danger: Could One Health help to cope with this threat to global health?

Planetary health faces an emergency associated with global change. Climate change, the increase in world population and urban concentration, the hyperintensification of productive systems, and the associated changes in land use, among other factors, are generating a risky substrate for global health deterioration. The emergence of the coronavirus disease 2019 pandemic is an example of the problems that this situation can provoke. Several researchers and health professionals have addressed the role of microorganisms, particularly bacteria, in promoting global health, mainly in the past decades. However, global changes have contributed to the extinction of a wide array of bacterial species and the disruption of microbial communities that support the homeostasis of humans, animals, and the environment. The need to protect the diversity and richness of native microbiomes in biotic and abiotic environments is crucial but has been frequently underestimated. The "One Health" approach, based on integrating traditionally unconnected fields such as human, animal, and environmental health, could provide a helpful framework to face this challenge. Anyway, drastic political decisions will be needed to tackle this global health crisis, in which the preservation of native microbial resources plays a critical role, even in preventing the risk of a new pandemic. This review aims to explain the importance of native microbiomes in biotic and abiotic ecosystems and the need to consider bacterial extinction as a crucial problem that could be addressed under a One Health approach.

Microbiome Forensic Biobanking: A Step toward Microbial Profiling for Forensic Human Identification

In recent years many studies have highlighted the great potential of microbial analysis in human identification for forensic purposes, with important differences in microbial community composition and function across different people and locations, showing a certain degree of uncertainty. Therefore, further studies are necessary to enable forensic scientists to evaluate the risk of microbial transfer and recovery from various items and to further critically evaluate the suitability of current human DNA recovery protocols for human microbial profiling for identification purposes. While the establishment and development of microbiome research biobanks for clinical applications is already very structured, the development of studies on the applicability of microbiome biobanks for forensic purposes is still in its infancy. The creation of large population microbiome biobanks, specifically dedicated to forensic human identification, could be worthwhile. This could also be useful to increase the practical applications of forensic microbiology for identification purposes, given that this type of evidence is currently absent from most real casework investigations and judicial proceedings in courts.

Cryopreservation of the human gut microbiota: Current state and perspectives

The human intestinal microbiota is a complex ecosystem that consists of thousands of bacterial species that are responsible for human health and disease. The intestinal microbiota is a natural resource for production of therapeutic and preventive medicals, such as probiotics and fecal transplants. Modern lifestyles have resulted in the extinction of evolutionally selected microbial populations upon exposure to environmental factors. Therefore, it is very important to preserve the human gut microbiota to have the opportunity for timely restoration with minimal safety risks. Cryopreservation techniques that are suitable for the preservation of viable, mixed microbial communities and a biobanking approach are currently under development in different countries. However, the number of studies in this area is very limited. The variety of morphological and physiological characteristics of microbes in the microbiota, the different cryopreservation goals, and the criteria for the evaluation of cryopreservation effectiveness are the main challenges in the creation of a universal and standardized cryopreservation protocol. In this review, we summarized the current progress of the main cryopreservation techniques for gut microbiota communities and the methods for the assessment of the effectiveness of these techniques in the context of practical application.

Comparative analysis of intestinal bacteria among venom secretion and non-secrection snakes

To further investigate the bacterial community and identify the bacterial biomarkers between venom secretion and non-venom secretion snakes, 50 intestinal samples (25 large intestine, 25 small intestine) were obtained from 29 snakes (13 gut samples from Deinagkistrodon, 26 from Naja and 11 from Ptyas mucosa). 16S rDNA high-throughput sequencing results showed that 29 bacterial phyla, 545 bacterial genera, and 1,725 OTUs (operational taxonomic units) were identified in these samples. OTU numbers and the Ace, Chao, Shannon, and Simpson indexes were very similar among the three breeds of snakes included in this study. The Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria were predominant bacterial phyla. The relative abundance at the phylum level among these samples was similar, and the difference between small and large intestinal samples was not obvious. However, at the genus level, venom secretion snakes Deinagkistrodon and Naja clustered together according to different breeds. 27, 24, and 16 genera were identified as core microbes for Deinagkistrodon, Naja, and Ptyas mucosa, respectively. Interestingly, the relative abundances of genera Hafnia_Obesumbacterium, Providencia, and Ureaplasma were found to be significantly higher in non-venom secretion snakes, and the genera Achromobacter, Cetobacterium, Clostridium innocuum group, Fusobacterium, Lachnoclostridium, Parabacteroides, and Romboutsia were only detected in venom secretion snakes. The function of these bacteria in venom secretion needs to be further studied, and these venom secretion related genera may be the promising target to improve venom production.