Culture-based and culture-independent approach for the study of the methanogens and obligate anaerobes from different landfill sites

The landfill is a cheap way of solid waste management in developing countries. The majority of landfills are non-sanitary and work as open garbage dumping sites and pose threats to public and environmental health. Therefore, an in-depth understanding of the chemistry and microbiology of landfills is imperative to develop the right policies for landfill management. In the current study, we investigated the chemistry and microbiology of three Indian landfill sites using culture-based and culture-independent molecular approaches. Our data indicate that the nature of landfills varies from site to site in terms of chemistry, pollutants, and pathogens. We also enriched and cultivated three methanogens using an optimized medium and constructed two high-quality draft genomes from enriched microbiomes using metagenome-assembled genome approaches. The phylogenomic study of one draft genome showed the highest 93% sequence similarity with members of Methanomassiliicoccaceae and was always enriched with Acholoplasma and Anaerohalosphaera lusitana. Despite all the efforts, we did not isolate it in pure culture and hypothesized that for the cultivation of some not-yet-cultured methanogen, the presence of other organisms plays an important role, and their syntrophic interaction must be discerned for its successful cultivation in the future. Co-cultivation of amino acid-degrading organisms indicates that their co-culture can assist in boosting the growth of methanogens. In addition, our data indicated that landfill leachate contains a heavy load of pollutants and treatment is a must before discharge in nature or use in irrigation or biofertilizer.

Vagococcus proximus sp. nov. and Vagococcus intermedius sp. nov., originating from modified atmosphere packaged broiler meat

During our studies on spoilage microbiomes of modified atmosphere packaged broiler meat, we isolated three strains (PNs007^T, STAA11^T and STAA25) of unknown identity. In this present polyphasic taxonomy study, including genome-based analyses, we discovered that these isolates represent two novel species belonging to the genus Vagococcus. In all phylogenetic analyses, PNs007^T was positioned very close to Vagococcus fessus but both the average nucleotide identity (ANI; 89.5 %) and digital DNA-DNA hybridization (dDDH; 38.3 %) values distinguished it as a novel vagococcal species. STAA11^T and STAA25 were genetically highly similar (16S rRNA, ANI and dDDH 100 %). The phylogenetic position of STAA11^T was adjacent to but out of the cluster containing V. fessus, Vagococcus coleopterorum and PNs007^T. According to the ANI (76.2-76.4 %) and dDDH (<22.6 %) values it also represented a novel vagococcal species. Phenotypic characteristics and chemotaxonomic properties of both novel species were typical for vagococci and they contained C_16 : 0 (25.5-30.1 %) and C_18 : 1 ω9c (67.3-73.0 %) as the major cellular fatty acids. The streptomycin-resistant genotype of STAA11^T and STAA25 allowing the growth on streptomycin thallous acetate actidione medium was considered to result from a modification in codon 104 of the rpsL gene leading to P104A substitution. The ability of STAA11^T and STAA25 to produce ammonia from arginine separated them from PNs007^T, which did not show arginine deiminase activity. We propose the names Vagococcus proximus sp. nov. (type strain PNs007^T=DSM 115185^T=CCUG 76696^T) and Vagococcus intermedius sp. nov. (type strain STAA11^T=DSM 115183^T=CCUG 76697^T) for these novel species.

Cultured and uncultured microbial community associated with biogas production in anaerobic digestion processes

The search for sustainable development has increased interest in the improvement of technologies that use renewable energy sources. One of the alternatives in the production of renewable energy comes from the use of waste including urban solids, animal excrement from livestock, and biomass residues from agro-industrial plants. These materials may be used in the production of biogas, making its production highly sustainable and environmentally friendly. The present study aimed to evaluate the cultivated and uncultivated microbial community from a substrate (starter) used as an adapter for biogas production in anaerobic digestion processes. 16S rDNA metabarcoding revealed the domain of bacteria belonging to the phyla Firmicutes, Bacteroidota, Chloroflexi and Synergistota. The methanogenic group was represented by the phyla Halobacterota and Euryarchaeota. Through 16S rRNA sequencing of isolates recovered from the starter culture, the genera Rhodococcus (Actinobacteria phylum), Vagococcus, Lysinibacillus, Niallia, Priestia, Robertmurraya, Proteiniclasticum (Firmicutes phylum), and Luteimonas (Proteobacteria phylum) were identified, genera that were not observed in the metabarcoding data. The volatile solids, volatile organic acids, and total inorganic carbon reached 659.10 g kg^-1, 717.70 g kg^-1, 70,005.0 g kg^-1, respectively. The cultured groups are involved in the metabolism of sugars and other compounds derived from lignocellulosic material, as well as in anaerobic methane production processes. The results demonstrate that culture-dependent approaches, such as isolation and sequencing, and culture-independent studies, such as the Metabarcoding approach, are complementary methodologies that, when integrated provide robust and comprehensive information about the microbial communities involved in processes of the production of biogas in anaerobic digestion processes.

The potentials of secondary metabolites from Bacillus cereus SN7 and Vagococcus fluvialis CT21 against fish pathogenic bacteria

One of the major factors that affect the total production of fisheries is the declining number of catches and aquaculture production due to the high pathogenicity in aquatic environment. This enforces the need to find anti-pathogenic agents that could solve the problem. In addition, the application of potential Bacillus cereus SN7 and Vagococcus fluvialis CT21 isolated and identified from the sea water of Siak, Riau, Indonesia need to be optimally exploited. The aim of this study, therefore, is to determine the component of bioactive compounds present in Bacillus cereus SN7 and Vagococcus fluvialis CT21, and also to explore their intrinsic potential as a biological control agent in fisheries, especially for inhibiting the growth of pathogenic bacteria (Vibrio alginolyticus, Aeromonas hydrophila and Pseudomonas aeruginosa). The method used was experimental, where the ethyl acetate crude extracts of both samples were analyzed for their phytochemical content, followed by thin layer chromatography analysis and Liquid Chromatography Mass Spectrometry. In addition, anti-pathogenic activity test was performed using the Kirby-Bauer method, minimum inhibitory and bactericidal concentration analysis. The results showed alkaloids, flavonoids, and saponins were the potential bioactive components in the crude extracts of Bacillus cereus SN7 and Vagococcus fluvialis CT21. Furthermore, the anti-pathogenic activity test demonstrated the ability for both bacteria to inhibit three types of pathogens with the following inhibitory zone values: Vibrio alginolyticus (10-11 mm), Aeromonas hydrophila (8-12 mm), and Pseudomonas aeruginosa (8-10 mm). In conclusion secondary metabolite compounds produced by Bacillus cereus SN7 and Vagococcus fluvialis CT21 possess the capacity to inhibit pathogenic bacteria. Hence, both samples are potential candidates for anti-pathogen development, especially in fisheries.

Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended description of the genus Vagococcus

A polyphasic taxonomic approach was used to characterize two novel bacterial strains, HDW17A^T and HDW17B^T, isolated from the intestine of the diving beetle Cybister lewisianus, and the dark diving beetle Hydrophilus acuminatus, respectively. Both strains were Gram-positive and facultative anaerobic cocci forming cream-colored colonies. The isolates grew optimally at 25°C, pH 7, in the presence of 0.3% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences showed that the isolates were members of the genus Vagococcus, and strain HDW17A^T was closely related to Vagococcus fessus CCUG 41755^T (98.9% of 16S rRNA gene sequence similarity and 74.3% of average nucleotide identity [ANI]), whereas strain HDW17B^T was closely related to Vagococcus fluvialis NCFB 2497^T (98.9% of 16S rRNA gene sequence similarity and 76.6% of ANI). Both strains contained C_16:0, and C_18:1ω9c as the major cellular fatty acids, but C_16:1ω9c was also observed only in strain HDW17B^T as the major cellular fatty acid. The respiratory quinone of the isolates was MK-7. The major polar lipid components were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The genomic DNA G + C content of strains HDW17A^T and HDW17B^T were 36.6 and 34.4%, respectively. Both strains had cell wall peptidoglycan composed of the amino acids L-alanine, glycine, D-glutamic acid, L-tryptophan, L-lysine, and L-aspartic acid, and the sugars ribose, glucose, and galactose. Based on phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, strains HDW17A^T and HDW17B^T represent two novel species in the genus Vagococcus. We propose the name Vagococcus coleopterorum sp. nov. for strain HDW17A^T (= KACC 21348^T = KCTC 49324^T = JCM 33674^T) and the name Vagococcus hydrophili sp. nov. for strain HDW17B^T (= KACC 21349^T = KCTC 49325^T = JCM 33675^T).

Vagococcus zengguangii sp. nov., isolated from yak faeces

Two unknown Gram-stain-positive, catalase- and oxidasenegative, non-motile, and coccus-shaped bacteria, designated MN-17^T and MN-09, were isolated from yaks faeces (Bos grunniens) in the Qinghai-Tibet Plateau of China. 16S rRNA gene sequence-based comparative analyses revealed that the two strains were grouped within the genus Vagococcus, displaying the highest similarity with Vagococcus xieshaowenii CGMCC 1.16436^T (98.6%) and Vagococcus elongatus CCUG 51432^T (96.4%). Both strains grew optimally at 37°C and pH 7.0 in the presence of 0.5% (w/v) NaCl. The complete genome of MN-17^T comprises 2,085 putative genes with a total of 2,190,262 bp and an average G + C content of 36.7 mol%. The major fatty acids were C_16:0 (31.2%), C_14:0 (28.5%), and C_18:1ω9c (13.0%); the predominant respiratory quinone was MK-7 (68.8%); the peptidoglycan type was A4α(L-Lys-D-Asp); and the major polar lipid was diphosphatidylglycerol. Together, these supported the affiliation of strain MN-17^T to the genus Vagococcus. In silico DNA-DNA hybridization and the average nucleotide identity values between MN-17^T and all recognized species in the genus were 21.6-26.1% and 70.7-83.0%, respectively. MN-17^T produced acid from D-cellobiose, D-fructose, glycerol, D-glucose, N-acetyl-glucosamine, gentiobiose, D-mannose, D-maltose, D-ribose, D-saccharose, salicin, D-trehalose, and D-xylose. These results distinguished MN-17^T and MN-09 from closely related species in Vagococcus. Thus, we propose that strains MN-17^T and MN-09 represent a novel species in the genus Vagococcus, with the name Vagococcus zengguangii sp. The type strain is MN-17^T (= CGMCC 1.16726^T = GDMCC 1.1589^T = JCM 33478^T).

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Biomethanation processes: new insights on the effect of a high H2 partial pressure on microbial communities

BACKGROUND

Biomethanation is a promising solution to upgrade the CH₄ content in biogas. This process consists in the injection of H₂ into an anaerobic digester, using the capacity of indigenous hydrogenotrophic methanogens for converting the injected H₂ and the CO₂ generated from the anaerobic digestion process into CH₄. However, the injection of H₂ could cause process disturbances by impacting the microbial communities of the anaerobic digester. Better understanding on how the indigenous microbial community can adapt to high H₂ partial pressures is therefore required.

RESULTS

Seven microbial inocula issued from industrial bioprocesses treating different types of waste were exposed to a high H₂ partial pressure in semi-continuous reactors. After 12 days of operation, even though both CH₄ and volatile fatty acids (VFA) were produced as end products, one of them was the main product. Acetate was the most abundant VFA, representing up to 94% of the total VFA production. VFA accumulation strongly anti-correlated with CH₄ production according to the source of inoculum. Three clusters of inocula were distinguished: (1) inocula leading to CH₄ production, (2) inocula leading to the production of methane and VFA in a low proportion, and (3) inocula leading to the accumulation of mostly VFA, mainly acetate. Interestingly, VFA accumulation was highly correlated to a low proportion of archaea in the inocula, a higher amount of homoacetogens than hydrogenotrophic methanogens and, the absence or the very low abundance in members from the Methanosarcinales order. The best methanogenic performances were obtained when hydrogenotrophic methanogens and Methanosarcina sp. co-dominated all along the operation.

CONCLUSIONS

New insights on the microbial community response to high H₂ partial pressure are provided in this work. H₂ injection in semi-continuous reactors showed a significant impact on microbial communities and their associated metabolic patterns. Hydrogenotrophic methanogens, Methanobacterium sp. or Methanoculleus sp. were highly selected in the reactors, but the presence of co-dominant Methanosarcinales related species were required to produce higher amounts of CH₄ than VFA.

Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content

A Gram-stain-positive, coccus-shaped, non-motile bacterium, designated CF-49^T, was isolated from the cloacal content of a snow finch, which was incidentally captured in a plateau pika burrow on the Qinghai-Tibet Plateau, PR China. Analysis of the 16S rRNA gene sequence showed that strain CF-49^T was closely related to Vagococcus elongatus CCUG 51432^T (96.5 % similarity), Vagococcus fluvialis NCFB 2497^T (96.0 %) and Vagococcus lutrae CCUG 39187^T (95.9 %), whereas the similarity to another isolate (CF-210) was 99.9 %. Strains CF-49^T and CF-210 grew optimally at 37 °C and pH 7.0 and in the presence of 0.5 % (w/v) NaCl. Acid was produced from N-acetylglucosamine, cellobiose, d-fructose, d-glucose, d-mannose, d-mannitol, maltose, d-ribose and salicin. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp). The major cellular fatty acids (>10 %) were C_16 : 0 (35.6 %), C_14 : 0 (17.3 %), C_18 : 1 ω9c (16.2 %) and C_16 : 1 ω9c (10.6 %). The predominant respiratory quinone was menaquinone MK-7 (68.8 %). The G+C content of the genomic DNA was 35.9 mol%. Digital DNA-DNA hybridization of strain CF-49^T with V. fluvialis DSM 5731^T, V. elongatus CCUG 51432^Tand V. lutrae CCUG 39187^T resulted in relatedness values of 21.4, 23.3 and 24.6 %, respectively. Based on results from polyphasic analyses, our two isolates are proposed to represent a novel species in the genus Vagococcus, with the name Vagococcus xieshaowenii. The type strain is CF-49^T (=CGMCC 1.6436^T=GDMCC 1.1588^T=JCM 33477^T).

Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound

Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994^T was isolated from ground beef and strain SS1995^T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994^T and SS1995^T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994^T showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995^T (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995^T was most similar to V. penaei (99.1 %), followed by SS1994^T (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %). A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994^T and SS1995^T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA-DNA hybridization <28 % to any other Vagococcus species. The names Vagococcusbubulae SS1994^T=(CCUG 70831^T=LMG 30164^T) and Vagococcusvulneris SS1995^T=(CCUG 70832^T=LMG 30165^T) are proposed.

Limited Effects of Low-to-Moderate Aerobic Exercise on the Gut Microbiota of Mice Subjected to a High-Fat Diet

Several studies have indicated that diet and exercise may modulate the gut microbiota in obese subjects. Both interventions were shown to alter the microbiota orthogonally. However, this relationship has not been fully explored. This study analyzed the effects of low-to-moderate aerobic training on the fecal microbiota of mice subjected to a high-fat diet (HFD). Here, 40 male mice (C57Bl/6) were divided into two groups with standard diet (SD; 12.4% lipid) and HFD (60.3% lipid) for four months. These groups were divided into four, named SD control, HF control, SD trained and HF trained. All animals were submitted to an incremental test to estimate low-to-moderate maximum speed. Training consisted of 30 min·day⁻¹, 5 days/week, for 8 weeks. The HFD increased the body weight (p < 0.0001) and adiposity index (p < 0.05). HFD also negatively influenced performance in exercise training. Moreover, the diversity of gut microbiota was reduced by the HFD in all groups. A low-to-moderate exercise was ineffective in modulating the gut microbiota composition in mice subjected to HFD. These findings suggest that two months of low-to-moderate exercise does not achieve a preponderant modulatory effect on shaping microbiota when submitted to the high-fat diet.

Potential of Bacterial Isolates from a Stream in Manaus-Amazon to Bioremediate Chromium-Contaminated Environments

Igarapé do Quarenta (IgQ), a stream located in the Manaus-AM, BR, has directly experienced the impacts of urban expansion over the last five decades, which contributed for its contamination. As an affluent of Rio Negro, IgQ also affects the water quality of this important river that bathes Manaus. However, the stress caused by the prolonged exposition to chemical agents may have selected microorganisms that exhibit great bioremediation potential. In the present study, bacteria isolated from four distinct sites of the IgQ were identified, and their potential to degrade hexavalent chromium (Cr(VI)) was investigated using the s-diphenylcarbazide method. Among the investigated isolates, 14 exhibited resistance against Cr(VI) at a concentration of 300 mg/L and eight isolates reduced over 50% (53.5-97.4%) chromium ratios after 72 h of incubation. Those isolates were identified by gene sequencing and classified in 10 genera (Acidovorax sp., Acinetobacter sp., Alicycliphilus sp., Bacillus sp., Comamonas sp., Enterobacter sp., Micrococcus sp., Proteus sp., Serratia sp., and Vagococcus sp.). Under control conditions, the isolate of Vagococcus sp. genus, in only 24 h of incubation, reduced 96.8% of the rate of Cr(VI) added to the culture medium at the concentration of 10 mg/L. Obtained results indicate that the Vagococcus sp. exhibits a great potential to be used in the bioremediation of areas contaminated with chromium. The mechanisms of action of microorganisms should be investigated for more specific applications in the decontamination of effluents and direct use of its by-products to bioremediate polluted environments.

Vagococcus humatus sp. nov., isolated from soil beneath a decomposing pig carcass

A Gram-stain-positive, non-motile, coccus-shaped bacterium, designated strain C25T, was isolated from the soil beneath a decomposing pig carcass in Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain C25T belongs to the genus Vagococcus in the family Enterococcaceae of the Lactobacillales. 16S rRNA gene sequence analysis showed that strain C25T was closely related to Vagococcus lutrae CCUG 39187T (96.5 % similarity) and Enterococcus termitis LMG 8895T (95.8 %). The chemotaxonomic properties of strain C25T were consistent with those of the genus Vagococcus; the major cellular fatty acids consisted of C16 : 0, C16 : 1ω9c and C18 : 1ω9c, and the cell-wall peptidoglycan type was based on meso-diaminopimelic acid. The G+C content of the genomic DNA was 44 mol%. On the basis of phylogenetic inference, fatty acid profile, and chemotaxonomic and other phenotypic properties, strain C25T is clearly differentiated from closely related type strains of the genus Vagococcus and represents a novel species in this genus, for which the name Vagococcus humatus sp. nov. is proposed. The type strain is C25T (=KEMB 562-002T=JCM 31581T).

Vagococcus entomophilus sp. nov., from the digestive tract of a wasp (Vespula vulgaris)

Three unknown Gram-stain-positive, catalase-negative, facultatively anaerobic and coccus-shaped strains of bacteria were isolated from the digestive tracts of wasps (Vespula vulgaris). Analysis of 16S rRNA gene sequences revealed that these strains had identical sequences and showed that Vagococcus salmoninarum , with 96.2 % sequence similarity, was the closest phylogenetic neighbour. Further analyses based on hsp60 and pheS gene sequences of representatives of the family Enteroccocaceae and genotypic and phenotypic characterization using (GTG)5-PCR fingerprintings, EcoRI ribotyping, DNA G+C content, whole-cell protein profiling, cellular fatty acid profiles analysis and extensive biotyping confirmed that the investigated strains were representatives of a novel bacterial species within the genus Vagoccocus for which the name Vagoccocus entomophilus sp. nov. is proposed. The type strain is VOSTP2T ( = DSM 24756T = CCM 7946T).

High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides

Vagococci are usually isolated from marine hosts and occasionally from endodontic infections. Using 16S rRNA gene comparison, the closest relatives are members of the genera Enterococcus and Carnobacterium. A draft sequence of Vagococcus lutrae was generated to clarify the relationship of Vagococcus to these and other related low-G+C Gram-positive bacteria.