Gut Samples Research Articles

Absolute quantification of the microbiota spatial distribution in the murine large intestine

<p>The species diversity, abundance, and location of intestinal bacteria bear major consequences on host intestinal functions, affecting the balance between health and disease. Recent studies addressed the relative abundance of bacteria in feces and on the gut mucosal surface. However, few of these publications reported the absolute number of bacteria in different compartments of the gut, especially those associated with the intestinal epithelial surface, compared to the luminal content reflected by feces. In this study, the number of bacteria present in the lumen or associated with the mucosal surface of mice gut samples was calculated using the bacterial ��internal standard method�� during sequencing. Three spiking bacteria were used for mutual corroboration. The microbiota spatial distribution in the cecum, proximal and distal colon were studied in the lumen content and gut wall fixed niches. This study also provides an example to demonstrate that absolute and relative quantification may yield different conclusions. This study��s method may eliminate such misjudgments and provide insight into the distribution and quantity of gut microbiome.</p>

Should the Christmas Island shrew (Crocidura trichura) be considered extinct?

The Christmas Island shrew (Crocidura trichura), endemic to Christmas Island in the Indian Ocean, was abundant at the time of the island’s settlement in the 1890s. However, since 1900, it has been reported only four times (twice in 1958, 1984 and 1985). It is currently considered Critically Endangered under Australian law. Using a recently developed IUCN protocol (the ‘Records and Surveys Model’), based on compilation and assessments of targeted and general sampling effort and detectability, we estimated that there is a 96.3% likelihood that the species is now extinct. However, although many general survey methods (including inspection of cat gut samples, ink cards, audio-recording, pitfall traps, spotlighting and camera traps) have been employed on Christmas Island, most recent sampling has not been targeted specifically to detect this species. Furthermore, there is considerable uncertainty about its likely detectability with different sampling techniques and hence much uncertainty about the estimate of likelihood of extinction. e-DNA sampling, use of detector dogs and refinements in audio-recording may help increase the likelihood of detection, if present. Most current conservation management actions, undertaken for other threatened species on Christmas Island, would provide benefit to the Christmas Island shrew, if it is extant.

A Novel Risk-Based Quantifiable Approach to Biosecurity Measures in Biofloc Units of West Bengal, India: Implications for Consumer Safety

A novel risk-based weighted scoring system was developed taking the risk of biosecurity measures of each biofloc technology (BFT) unit in two aquaculturally influential districts, North and South 24 Parganas, West Bengal, India, into account. The current study was carried out over a 6-month period to observe the incidence of Aeromonas veronii and Escherichia coli in biofloc units of these districts along with a questionnaire-based survey on biosecurity measures employed there. Moreover, the correlation between the total heterotrophic bacterial counts (THBCs) in water and gut with the physicochemical parameters of water was also analyzed. The physico-chemical parameters of water in the BFT units were maintained optimally for Nile tilapia culture. A significant positive correlation was observed between the THBCs of water samples and the dissolved oxygen (DO) of Panchpota unit, whereas a significantly negative correlation was observed between the THBCs of water and gut samples collected from Basirhat and Ashoknagar units. The prominence of E. coli in biofloc units of South 24 Parganas suggested possible faecal contamination and lower biosecurity measures being implemented implying at the threats of consumer safety. The grading system, on the other hand, might be viewed as a beneficial instrument for monitoring the biosecurity level of biofloc units over time and pointed out that West Bengal biofloc farmers paid more heed to internal biosecurity than external biosecurity measures.

Probiotic Debaryomyces hansenii CBS 8339 yeast enhanced immune responses in mice.

This study aimed to examine the effect of Debaryomyces hansenii CBS 8339 on innate immune responses in mice. Thirty BALB/c mice were randomly treated with phosphate buffered saline (PBS) (control) and two D. hansenii (Dh) doses: Dh 10ˆ6 CFU (colony forming units) and Dh 10ˆ8 CFU daily for 15days. Spleen, blood, and gut samples were taken on days7 and 15. Mouse splenocytes were isolated and challenged with Escherichia coli. Immunological assays and immune-related gene expressions were performed. Serum was obtained from blood for total IgA and IgG antibody titer determination. Gut samples were taken for yeast colonization assessment. Phagocytosis, respiratory burst activity, and nitric oxide production in mice were mainly enhanced (p < 0.05) upon 7days of D. hansenii intake at a concentration of 10ˆ8 CFU before and after bacterial challenge. Moreover, oral D. hansenii in mice upregulated (p < 0.05) gene expression of pro-inflammatory cytokines (INF-γ, IL-6 and IL-1β) before or after E. coli challenge on day7 but downregulated (p < 0.05) on day15. Furthermore, total serum IgG and IgA titers were higher (p < 0.05) in Dh 10ˆ8 CFU at days7 and 15, and only at day7, respectively, than that in the other dose and control groups. Finally, D. hansenii was detected in the gut of mice that received the treatments, suggesting that yeast survived gastrointestinal transit. Altogether, a short period (7days) of D. hansenii CBS 8339 oral delivery improved immune innate response on mice.

Dietary Association with Midgut Microbiota Components of Eocanthecona furcellata (Wolff)

Eocanthecona furcellata is an important predatory stinkbug that attacks many lepidopteran pests. For mass-rearing, artificial diets are used to rear this predator in the laboratory; however, the fitness of the predators is reduced, and little is known about the cause. Since gut microbiota plays vital roles in the digestion and development of many hosts and can consequently affect host fitness, an understanding of the microbial community composition of E. furcellata may help to solve this unresolved problem. We compared the development and reproduction of E. furcellata reared on an artificial diet, and a natural (Spodoptera litura) or semi-natural (Tenebrio molitor) diet, and then the midgut microbiota were assessed using high-throughput 16S rRNA. The results of the high-throughput 16S rRNA show that the bacterial richness and diversity in the artificial diet gut samples increased considerably compared with the other samples. Proteobacteria and Firmicutes were the dominant phyla in E. furcellata. At the genus level, Serratia (however, the relative abundance was lower in the artificial diet gut samples), Enterococcus, and an uncultured bacterium genus of family Enterobacteriaceae, were dominant. The midgut microbiota components significantly differed among the diets, indicating that the gut bacteria had a dietary association with E. furcellata. This study provides a better understanding of midgut microbiota and the artificial diets that might affect them in E. furcellata.

Dysbiosis: An Indicator of COVID-19 Severity in Critically Ill Patients

Here, we examined the dynamics of the gut and respiratory microbiomes in severe COVID-19 patients in need of mechanical ventilation in the intensive care unit (ICU). We recruited 85 critically ill patients (53 with COVID-19 and 32 without COVID-19) and 17 healthy controls (HCs) and monitored them for up to 4 weeks. We analyzed the bacterial and fungal taxonomic profiles and loads of 232 gut and respiratory samples and we measured the blood levels of Interleukin 6, IgG, and IgM in COVID-19 patients. Upon ICU admission, the bacterial composition and load in the gut and respiratory samples were altered in critically ill patients compared with HCs. During their ICU stay, the patients experienced increased bacterial and fungal loads, drastic decreased bacterial richness, and progressive changes in bacterial and fungal taxonomic profiles. In the gut samples, six bacterial taxa could discriminate ICU-COV(+) from ICU-COV(-) cases upon ICU admission and the bacterial taxa were associated according to age, PaO2/FiO2, and CRP levels. In the respiratory samples of the ICU-COV(+) patients, bacterial signatures including Pseudomonas and Streptococcus were found to be correlated with the length of ICU stay. Our findings demonstrated that the gut and respiratory microbiome dysbiosis and bacterial signatures associated with critical illness emerged as biomarkers of COVID-19 severity and could be a potential predictor of ICU length of stay. We propose using a high-throughput sequencing approach as an alternative to traditional isolation techniques to monitor ICU patient infection.

Multi-omics analyses reveal that the gut microbiome and its metabolites promote milk fat synthesis in Zhongdian yak cows.

Yak cows produce higher quality milk with higher concentrations of milk fat than dairy cows. Recently, studies have found the yak milk yield and milk fat percentage have decreased significantly over the past decade, highlighting the urgency for yak milk improvement. Therefore, we aimed to analyze how the gut microbiome impacts milk fat synthesis in Zhongdian yak cows. We collected milk samples from Zhongdian yak cows and analyzed the milk fat percentage, selecting five Zhongdian yak cows with a very high milk fat percentage (>7%, 8.70±1.89%, H group) and five Zhongdian yak cows with a very low milk fat percentage (<5%, 4.12±0.43%, L group), and then obtained gut samples of these ten Zhongdian yak cows through rectal palpation. Gut metagenomics, metabolomics, and conjoint metagenomics and metabolomics analyses were performed on these samples, identifying taxonomic changes, functional changes, and changes in gut microbes-metabolite interactions within the milk fat synthesis-associated Zhongdian yak cows gut microbiome, to identify potential regulatory mechanisms of milk fat at the gut microbiome level in Zhongdian yak cows. The metagenomics analysis revealed Firmicutes and Proteobacteria were significantly more abundant in the gut of the high-milk fat Zhongdian yak cows. These bacteria are involved in the biosynthesis of unsaturated fatty acids and amino acids, leading to greater efficiency in converting energy to milk fat. The metabolomics analysis showed that the elevated gut metabolites in high milk fat percentage Zhongdian yak cows were mainly enriched in lipid and amino acid metabolism. Using a combined metagenomic and metabolomics analysis, positive correlations between Firmicutes (Desulfocucumis, Anaerotignum, Dolosiccus) and myristic acid, and Proteobacteria (Catenovulum, Comamonas, Rubrivivax, Marivita, Succinimouas) and choline were found in the gut of Zhongdian yak cows. These interactions may be the main contributors to methanogen inhibition, producing less methane leading to higher-efficient milk fat production. A study of the gut microbe, gut metabolites, and milk fat percentage of Zhongdian yak cows revealed that the variations in milk fat percentage between yak cows may be caused by the gut microbes and their metabolites, especially Firmicutes-myristic acid and Proteobacteria-choline interactions, which are important to milk fat synthesis. Our study provides new insights into the functional roles of the gut microbiome in producing small molecule metabolites and contributing to milk performance traits in yak cows.

Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure.

We examined the effects of a mixture of contaminants found in agricultural watersheds on the gut microbiota and physiology of both the freshwater mussel Lampsilis cardium, and L. cardium host fish Micropterus salmoides. Lampsilis cardium and M. salmoides were exposed to three concentrations of agricultural contaminants for 60 days (observing behaviour daily) before being sampled for gut microbiota analyses. DNA was extracted from the gut samples, amplified via PCR, and sequenced using the Illumina Mi-Seq platform. Only L. cardium guts had differing microbiota across treatments, with an increase in potentially pathogenic Aeromonas. We also provide novel evidence of a core microbiota within L. cardium and M. salmoides. In terms of physiology, female L. cardium exhibited a decrease in movement and marsupial gill display in contaminant exposures. Exposure to contaminants from agricultural watersheds may affect population recruitment within freshwater mussel communities over time. Specifically, increased pathogenic micro-organisms and altered behaviour can reduce the likelihood of glochidia dispersal. This study supports emerging research that contaminants found in agricultural watersheds may be a factor in freshwater mussel population declines. It also provides novel evidence that unionids have a core gut microbiota.

Detection of extended spectrum beta lactam producing Escherichia coli isolated from Cyprinus carpio in Mosul city

Extended-spectrum b-lactamase (ESBL)-producing Escherichia coli constitute an emerging health problem globally, fish act as a potential reservoir for ESBLs E. coli and serve as a vehicle of transmission of ESBL resist genes to others strains of bacteria. A total of 75 samples of Cyprinus carpio were collected from the local fish market of Mosul city during the period between) October 2021 to February 2022(. each sample was placed separately in a sterile plastic bag and transported directly under cooling conditions to the microbiology lab, College of Veterinary Medicine. ESBLs producing Escherichia coli were isolated and characterized using MacConkey agar medium supplemented with 2 mcg/ml cefotaxime. Twenty-six isolates 34% of fish gut samples were obtained. A polymerase chain reaction was carried out to confirm the results of the isolation using special primers for E. coli (ECO223-f, ECO223-r). Resistance genes assay were performed using the primers Cefotaxamase (CTX-M) and sulphydryl variable (SHV). All isolates showed that possessed the CTX-M gene 100%, while none of the isolates possessed the SHV gene. This study showed that fish play a major role in the transmission of broad-spectrum beta-lactam-resistant Escherichia coli to humans as a result of handling or marketing it, or by consuming contaminated or infected fish.

Understanding dietary differences in Indian dugongs through opportunistic gut sampling of stranded individuals

Understanding dietary differences in Indian dugongs through opportunistic gut sampling of stranded individuals

Gut microbiota modulation by plant polyphenols in koi carp (Cyprinus carpio L.).

Plant polyphenol supplementation may improve fish health in aquaculture systems. To assess the potential benefits and function mechanism of plant polyphenols in aquaculture, fish were fed either basal feed (CON) or the basal feed supplemented with 500 mg/kg of curcumin (CUR), oligomeric proanthocyanidins (OPC), chlorogenic acid (CGA), or resveratrol (RES). After an 8-week feeding experiment, blood samples were used to analyze the concentrations of biochemical indices. Gut samples were collected to evaluate microbiota, short chain fatty acid (SCFA) levels, and gene expression. The results indicated that polyphenol administration reduced serum glucose and insulin. Lysozyme activity was enhanced by OPC and CGA, and superoxide dismutase activity was increased by CUR, OPC, and CGA. The gut microbial structure of the RES group was segregated from that of the CON, and the genus Bacteroides was identified as a potential biomarker in the CUR, CGA, and RES groups. Total gut SCFA increased in the CUR, CGA, and RES groups. A strong correlation was observed between Bacteroides and SCFA. In conclusion, dietary polyphenols have distinct anti-inflammatory, anti-oxidant, and anti-hyperglycemic activities that may be closely associated with their microbiota-modulation effects.

Microbiome data reveal significant differences in the bacterial diversity in freshwater rohu (Labeo rohita) across the supply chain in Dhaka, Bangladesh.

The present study aimed to characterize and compare the skin and gut microbial communities of rohu at various post-harvest stages of consumption using quantitative real-time polymerase chain reaction and 16S rRNA-based amplicon sequencing. Real-time PCR amplification detected higher copy numbers for coliform bacteria-Escherichia coli, Salmonella enterica and Shigella spp. in the marketed fish-compared to fresh and frozen samples. The 16S rRNA data revealed higher alpha diversity measurements in the skin of fish from different retail markets of Dhaka city. Beta ordination revealed distinct clustering of bacterial OTUs for the skin and gut samples from three different groups. At the phylum level, Proteobacteria was most abundant in all groups except the Fusobacteria in the control fish gut. Although Aeromonas was found ubiquitous in all types of samples, diverse bacterial genera were identified in the marketed fish samples. Nonetheless, low species richness was observed for the frozen fish. Most of the differentially abundant bacteria in the skin samples of marketed fish are opportunistic human pathogens enriched at different stages of postharvest handling and processing. Therefore, considering the microbial contamination in the aquatic environment in Bangladesh, post-harvest handling should be performed with proper methods and care to minimize bacterial transmission into fish.

Tracking spoilage bacteria in the tuna microbiome.

Like other seafood products, tuna is highly perishable and sensitive to microbial spoilage. Its consumption, whether fresh or canned, can lead to severe food poisoning due to the activity of specific microorganisms, including histamine-producing bacteria. Yet, many grey areas persist regarding their ecology, conditions of emergence, and proliferation in fish. In this study, we used 16S rRNA barcoding to investigate postmortem changes in the bacteriome of fresh and brine-frozen yellowfin tuna (Thunnus albacares), until late stages of decomposition (i.e. 120h). The results revealed that despite standard refrigeration storage conditions (i.e. 4°C), a diverse and complex spoilage bacteriome developed in the gut and liver. The relative abundance of spoilage bacterial taxa increased rapidly in both organs, representing 82% of the bacterial communities in fresh yellowfin tuna, and less than 30% in brine-frozen tuna. Photobacterium was identified as one of the dominant bacterial genera, and its temporal dynamics were positively correlated with histamine concentration in both gut and liver samples, which ultimately exceeded the recommended sanitary threshold of 50ppm in edible parts of tuna. The results from this study show that the sanitary risks associated with the consumption of this widely eaten fish are strongly influenced by postcapture storage conditions.

Activity fingerprinting of polysaccharides on oral, gut, pancreas and lung microbiota in diabetic rats

The modern rise in type 2 diabetes mellitus (T2DM) and its correlation to commensal microbiota have elicited global concern about the patterns of microbial action in the host. With the exception of that linked to gut, microbiota were also colonized in pancreas, oral, and lung, contributing to the physiopathology of T2DM. In this study, we aimed to explore the protective effects of Ganoderma atrum polysaccharide (PSG) and White Hyacinth Bean polysaccharide (WHBP) on the intestine, pancreas, oral, and lung microbiota in T2DM rats. Here we showed that, despite capacities of polysaccharides that exerted similar protective effects on hyperglycemia, dyslipidemia, insulin resistance and dysbacteriosis in T2DM rats, PSG and WHBP were able to be characterized by their own "target" bacteria, which could be proposed for activity-fingerprinting of polysaccharide species. Furthermore, we found a mutual bacteria spectrum in the pancreas and lung, and most bacteria could be tracked to oral or gut samples. Notably, the overlapping areas of the microbiota profile between organs (pancreas, lung) and saliva were more than in the gut, suggesting that a saliva sample was also of interest to serve as a "telltale sign" for judging pancreatic injury. Together, these microbiota interactions provided a new potential to harvest alternative samples for disease surveillance. Meanwhile, polysaccharides had anti-T2DM abilities, which could be distinguished by their own characteristic bacteria.

Do Changes in Prey Community in the Environment Affect the Feeding Selectivity of Silver Carp (Hypophthalmichthys molitrix) in the Pearl River, China?

Silver carp (Hypophthalmichthys molitrix) is a world-wide species and its ecosystem level influence is controversial. Therefore, understanding the feeding behaviour of silver carp is important for assessing ecosystem functioning in many freshwater habitats. In this study, we used 18S rRNA sequencing to identify the spatiotemporal taxonomic composition of water and fish gut samples. Significant seasonal and spatial variations were observed in the taxonomic compositions of water and fish gut samples (p &lt; 0.05). Five selected environmental factors (temperature, total phosphorus, chlorophyll a, ammonia, and distance from the first dam downstream) significantly affected the taxonomic composition of water (p &lt; 0.05). Additionally, the temperature was the most important factor affecting seasonal (winter and summer) variations in the prey community composition of water, whereas the distance from the dam was the key factor contributing to spatial differences in the community. Significant differences were observed in the taxonomic composition between the water and fish gut samples (p &lt; 0.05). Feeding selectivity analysis revealed that the selection ratios of the top 20 prey taxa underwent slight spatial and temporal changes, but silver carp always preferred to feed on Peridiniales, unidentified Streptophyta, unidentified Trebouxiophyceae, and unidentified Chlorophyceae. These results indicate that changes in the prey community in the environment affect the taxonomic composition of the fish gut but do not affect feeding preferences.

Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts

BackgroundSymbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts’ health. Traditional sequencing profiling masks the genomic and phenotypic diversity among strains from the same species. Innovative droplet-based microfluidic cultivation may help to elucidate the inter-strain interactions. A limited number of bacterial phylotypes colonize the honeybee gut, while individual strains possess unique genomic potential and critical capabilities, which provides a particularly good model for strain-level analyses.ResultsHere, we construct a droplet-based microfluidic platform and generated ~ 6 × 108 droplets encapsulated with individual bacterial cells from the honeybee gut and cultivate in different media. Shotgun metagenomic analysis reveals significant changes in community structure after droplet-based cultivation, with certain species showing higher strain-level diversity than in gut samples. We obtain metagenome-assembled genomes, and comparative analysis reveal a potential novel cluster from Bifidobacterium in the honeybee. Interestingly, Lactobacillus panisapium strains obtained via droplet cultivation from Apis mellifera contain a unique set of genes encoding l-arabinofuranosidase, which is likely important for the survival of bacteria in competitive environments.ConclusionsBy encapsulating single bacteria cells inside microfluidic droplets, we exclude potential interspecific competition for the enrichment of rare strains by shotgun sequencing at high resolution. The comparative genomic analysis reveals underlying mechanisms for host-specific adaptations, providing intriguing insights into microbe-microbe interactions. The current approach may facilitate the hunting for elusive bacteria and paves the way for large-scale studies of more complex animal microbial communities.6MWJv9N2gCCgq2b2j_Wic-Video

Dysbiotic Oral and Gut Viromes in Untreated and Treated Rheumatoid Arthritis Patients.

ABSTRACTRheumatoid arthritis (RA) is influenced by oral and gut bacteria; however, much less is known about the relationship between oral or gut viromes and RA. Here, we performed whole-oral- and whole-gut-virome analyses based on shotgun sequencing of 497 samples. A comparative analysis of the oral and gut viromes in healthy controls and untreated and treated RA patients was performed, and system interaction networks among viruses, bacteria, and RA-associated clinical indices were constructed to address the potential relationship between the virome and RA by principal-coordinate analysis, distance-based redundancy analysis, permutational multivariate analysis, Spearman correlation coefficient analysis, and random-forest model analysis. The results showed that the viromes could be profiled in dental plaque, saliva, and fecal samples, among which saliva had the highest within-sample diversity. Importantly, significantly different diversities and compositions of the oral (i.e., dental plaque and saliva) viromes were observed not only between RA patients and healthy controls but also between untreated and treated RA patients, yet there were relatively minor differences in the gut viromes. Furthermore, to understand how these viruses affected the bacteriome, a virus-bacterium interaction network was constructed from dental plaque, saliva, and fecal samples of RA patients. Additionally, some RA-associated oral taxa, including Lactococcus phage (vOTU70), Bacteroides vulgatus, Lactococcus lactis, Escherichia coli, and Neisseria elongata, were correlated with the RA-related clinical indices. Whole-virome analysis illustrated the potential role of the oral and gut viromes in affecting our body either directly or via bacteria, which characterized neglected and new candidates contributing to the development of RA.IMPORTANCE Our results demonstrated community variation among dental plaque, saliva, and fecal viromes. In oral and gut samples from untreated and treated RA patients, the perturbance of viral composition and the correlation network of microbes and RA-associated clinical indices might be involved in the pathogenicity of RA. The findings in this study expand the knowledge of the potential role of oral and gut viral communities in the development of RA and may contribute to research on correlations between viruses and other diseases.

Northern pike (Esox lucius) young‐of‐year gut microbiota and associations with wetland nursery water microbial communities in the St. Lawrence River

AbstractThe core‐microbiome hypothesis postulates that key fish gut microbiota develop independently from the environment they exist in. Fish nursery habitats serve as critical environments early in ontogeny that support fish growth and development, but their relationship to the development of gut microbiota is poorly understood. We compared gut microbiota of first growing season northern pike (Esox lucius) and source water from two spatially distinct nursery wetlands to examine their potential association and as a field test of the core‐microbiome hypothesis. Microbial communities within the pike hindguts and associated water column samples were characterized through metabarcoding and sequencing of the 16S rRNA gene. As expected, community level non‐metric multidimensional scaling analysis revealed significant separation in microbial community composition between fish and water samples. Unifrac distances indicated no significant dissimilarity among fish gut and source water combinations compared to fish gut samples pairwise tested with non‐source water samples, suggesting similar patterns of in vivo selection of the gut microbiome. This was consistent among habitats for three of four dominant hindgut bacterial genera (Aeromonas spp., Clostridium sensu stricto, and Plesiomonas spp.). Cetobacterium spp. was an exception, where they dominated fish guts in one wetland system. Because these four‐core gut microbiota were only minor components of the source water environment, it is possible that environmental exposure is a selective process in the developing fish gut. Further experimental and field research with examination of the influence of diet is needed to isolate mechanisms involved in gut microbiome development in freshwater fishes.

Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes.

Lactococcus lactis (L. lactis) is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of L. lactis from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of L. lactis by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of L. lactis. An open pangenome of L. lactis was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that L. lactis strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. Lactococcus lactis has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of L. lactis is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of L. lactis constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes. This study expanded the genetic information of L. lactis about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of L. lactis is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.

Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing.

Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors ‘Study’, ‘Age’ and ‘Feed’ (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.