ABSTRACT The medicinal leech, Hirudo verbana , is one of the simplest naturally occurring models for digestive-tract symbioses, where only two bacterial species, Aeromonas veronii bv. sobria (γ- Proteobacteria ) and a Rikenella -like bacterium ( Bacteroidetes ), colonize the crop, the largest compartment of the leech digestive tract. In this study, we investigated spatial and temporal changes of the localization and microcolony structure of the native symbionts in the crop, after ingestion of a sterile blood meal, by fluorescence in situ hybridization. The population dynamics differed between the two symbiotic bacteria. A. veronii was detected mainly as individual cells inside the intraluminal fluid (ILF) during 14 days after feeding (daf) unless it was found in association with Rikenella microcolonies. The Rikenella -like bacteria were observed not only inside the ILF but also in association with the luminal surface of the crop epithelium. The sizes of Rikenella microcolonies changed dynamically through the 14-day period. From 3 daf onward, mixed microcolonies containing both species were frequently observed, with cells of both species tightly associating with each other. The sizes of the mixed microcolonies were consistently larger than the size of either single-species microcolony, suggesting a synergistic interaction of the symbionts. Lectin staining with succinylated wheat germ agglutinin revealed that the planktonic microcolonies present in the ILF were embedded in a polysaccharide matrix containing N -acetylglucosamine. The simplicity, symbiont-symbiont interaction, and mixed microcolonies of this naturally occurring, digestive-tract symbiosis lay the foundation for understanding the more complex communities residing in most animals.
Background: Circulating inflammatory markers increase with age. This pro-inflammatory milieu makes the organism less capable of coping with stressors such as stroke. Age related inflammation occurs in both the brain and peripheral tissues like the gastro-intestinal tract. There is increasing recognition that commensal bacteria in the GI tract are altered with age or with germ-free housing, affecting the brain. The change occurs most notably in the ratio of two major phyla of the microbiome, the Firmicutes and Bacteroidetes . Young age is associated with a low ratio of the two but this ratio increases with age, which has been linked to many diseases including obesity, hypertension, and diabetes which are major risk factors for stroke. Hypothesis: We hypothesized that there would be age-related differences in the microbiome, and that restoration of a young microbiome would improve functional recovery in aged mice. Methods: Fecal transplants from young and aged donors were administered to recipient animals after suppression of endogenous microbial compositions through concentrated Streptomycin. This allowed for successful colonization of the gut with the newly transplanted microbiome. A transient middle cerebral artery occlusion (MCAO) was used in young (3-4 month) and aged (18-20 month) male mice 4 weeks after transplant. Functional recovery was assessed by neurological deficit scores, the hang wire test, and open field activity. The Y-maze was used to assess cognitive impairment. Results: We successfully reversed the microbiomes of aged organisms and gave young animals “aged” biomes. Animals with “aged” microbiomes prior to stroke had worsened functional recovery based on all behavioral tests. The “aged” biome increased mortality rates most notably in the young recipients which had over 50% mortality. Aged mice had significantly improved functional recovery as assessed by the HW test ( P < 0.05 ) and NDS after reconstitution of “young” microbiome prior to stroke compared to aged control animals with the normal “aged” microbiomes. Conclusion: Aged mice have high Firmicutes and Bacteroidetes relative abundances. Manipulation of the microbiome in young and aged mice is possible. Restoration of a youthful biome improved functional recovery in aged mice.
Identifying and tracking microbial strains as microbiomes evolve are major challenges in the field of microbiome research. We utilized a new sequencing kit that combines DNA extraction with PCR amplification of a large region of the rRNA operon and downstream bioinformatic data analysis. Longitudinal microbiome samples of coadmitted twins from two different neonatal intensive care units (NICUs) were analyzed using an ∼2,500-base amplicon that spans the 16S and 23S rRNA genes and mapped to a new, custom 16S-23S rRNA database. Amplicon sequence variants (ASVs) inferred using DADA2 provided sufficient resolution for the differentiation of rRNA variants from closely related but not previously sequenced Klebsiella, Escherichia coli, and Enterobacter strains, among the first bacteria colonizing the gut of these infants after admission to the NICU. Distinct ASV groups (fingerprints) were monitored between coadmitted twins over time, demonstrating the potential to track the source and spread of both commensals and pathogens. The high-resolution taxonomy obtained from long amplicon sequencing enables the tracking of strains temporally and spatially as microbiomes are established in infants in the hospital environment.IMPORTANCE Achieving strain-level resolution is a major obstacle for source tracking and temporal studies of microbiomes. In this study, we describe a novel deep-sequencing approach that provides species- and strain-level resolution of the neonatal microbiome. Using Klebsiella, E. coli, and Enterobacter as examples, we could monitor their temporal dynamics after antibiotic treatment and in pairs of twins. The strain-level resolution, combined with the greater sequencing depth and decreased cost per read of PacBio Sequel 2, enables this advantageous source- and strain-tracking analysis method to be implemented widely across more complex microbiomes.
Three anaerobic bacterial strains were isolated from the digestive tract of the medicinal leech Hirudo verbana, using mucin as the primary carbon and energy source. These strains, designated M3(T), M4 and M6, were Gram-stain-negative, non-spore-forming and non-motile. Cells were elongated bacilli approximately 2.4 µm long and 0.6 µm wide. Growth only occurred anaerobically under mesophilic and neutral pH conditions. All three strains could utilize multiple simple and complex sugars as carbon sources, with glucose fermented to acid by-products. The DNA G+C contents of strains M3(T), M4 and M6 were 44.9, 44.8 and 44.8 mol%, respectively. The major cellular fatty acid of strain M3(T) was iso-C15 : 0. Phylogenetic analysis of full-length 16S rRNA gene sequences revealed that the three strains shared >99 % similarity with each other and represent a new lineage within the family Rikenellaceae of the order Bacteroidales, phylum Bacteroidetes. The most closely related bacteria to strain M3(T) based on 16S rRNA gene sequences were Rikenella microfusus DSM 15922(T) (87.3 % similarity) and Alistipes finegoldii AHN 2437(T) (87.4 %). On the basis of phenotypic, genotypic and physiological evidence, strains M3(T), M4 and M6 are proposed as representing a novel species of a new genus within the family Rikenellaceae, for which the name Mucinivorans hirudinis gen. nov., sp. nov. is proposed. The type strain of Mucinivorans hirudinis is M3(T) ( = ATCC BAA-2553(T) = DSM 27344(T)).
We present the complete, closed, and finished chromosomal and extrachromosomal genome sequences of Yersinia ruckeri strain CSF007-82, the etiologic agent of enteric red mouth disease in salmonid fish. The chromosome is 3,799,036 bp with a G+C content of 47.5% and encodes 3,530 predicted coding sequences (CDS), 7 ribosomal operons, and 80 tRNAs.
Especially when combined with unique biological adaptations, invertebrate animals provide important insights into innate immunity because the immune response is not complicated by adaptive immunity that vertebrates evolved. One such example is the digestive tract of the medicinal leech, Hirudo verbana, which is unusual in two aspects, it contains a simple microbial community and it stores large amounts of vertebrate blood for a several months. In this review we will discuss aspects of the innate immunity of the leech and from the ingested blood that we term procured immunity to differentiate it from the immunity encoded by the leech genome.
Although many advances have been made in genome sequencing for analyzing the composition of microbiomes, very few studies have attempted to learn and model their dynamics. Furthermore, no studies have attempted to exploit the dynamics of compositional changes of a microbiome for overproducing a metabolite of interest. This task proves to be computationally difficult at best and intractable at worst. The challenge is due to the complex, interdependent, and large number of highly non-linear interactions among members of a microbiome, as well as environmental factors, e.g. substrate. Here, we present a computationally tractable strategy using machine learning methods and stochastic optimization to characterize and potentially engineer a microbiome. In this work, an artificial neural network (ANN) is utilized to learn how six different lignocellulose food sources affect the temporal composition of the hindgut microbiome of Reticulitermes flavipes, the eastern subterranean termite. The learned dynamics from the ANN are optimized using either a genetic algorithm or artificial immune system approach. Specifically, the optimization objective is the maximization of the Rhodospirillales, an acetate producing order of bacteria, which will intrinsically maximize acetate production from the microbiome. The genetic algorithm and artificial immune system are compared for robustness and speed.
ABSTRACT We announce the draft genome assembly of Lactococcus garvieae strain PAQ102015-99, a recently isolated strain from an outbreak of lactococcosis at a commercial trout farm in the northwestern United States. The draft genome comprises 14 contigs totaling 2,068,357 bp with an N 50 of 496,618 bp and average G+C content of 38%.
