Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus

Pre-treatment oral microbiome analysis and salivary Stephan curve kinetics in white spot lesion development in orthodontic patients wearing fixed appliances. A pilot study

BACKGROUND

White spot lesions (WSLs) are a formidable challenge during orthodontic treatment, affecting patients regardless of oral hygiene. Multifactorial in nature, amongst potential contributors to their development are the microbiome and salivary pH. The aim of our pilot study is to determine if pre-treatment differences in salivary Stephan curve kinetics and salivary microbiome features correlate with WSL development in orthodontic patients with fixed appliances. We hypothesize that non-oral hygiene determined differences in saliva could be predictive of WSL formation in this patient population through analysis of salivary Stephan curve kinetics, and that these differences would further manifest as changes in the oral microbiome.

METHODS

In this prospective cohort study, twenty patients with initial simplified oral hygiene index scores of "good" that were planning to undergo orthodontic treatment with self-ligating fixed appliances for at least 12 months were enrolled. At pre-treatment stage, saliva was collected for microbiome analysis, and at 15-minute intervals after a sucrose rinse over 45 min for Stephan curve kinetics.

RESULTS

50% of patients developed a mean 5.7 (SEM: 1.2) WSLs. There were no differences in saliva microbiome species richness, Shannon alpha diversity or beta diversity between the groups. Capnocytophaga sputigena exclusively and Prevotella melaninogenica predominantly were found in WSL patients, while Streptococcus australis was negatively correlated with WSL development. Streptococcus mitis and Streptococcus anginosus were primarily present in healthy patients. There was no evidence to support the primary hypothesis.

CONCLUSIONS

While there were no differences in salivary pH or restitution kinetics following a sucrose challenge and no global microbial differences in WSL developers, our data showed change in salivary pH at 5 min associated with an abundance of acid-producing bacteria in saliva. The results suggest salivary pH modulation as a management strategy to inhibit the abundance of caries initiators. Our study may have uncovered the earliest predecessors to WSL/caries development.

Simultaneous production of hydrogen-methane and spatial community succession in an anaerobic baffled reactor treating corn starch processing wastewater

Corn starch processing wastewater (CSPW) is a high-strength organic wastewater and biological treatment is considered as the dominant process. The present work investigated the effects of pH on the bioenergy production and spatial succession of microbial community in an anaerobic baffled reactor (ABR) treating CSPW. The results showed that above 90.5% of COD removal and above 16.6 L d^-1 of methane were achieved at the influent pHs of 8.0 and 7.0 under organic loading rate of 4.0 kg COD·m^-3·L^-1 condition. Further decreasing the influent pH to 6.0 resulted in the COD removal decreased to 89.7%. Besides, 9.2 L d^-1 of hydrogen and 13.0 L d^-1 of methane were obtained. There was significant difference in the volatile fatty acids profiles during the variation of pH. Illumina Miseq sequencing showed that Clostridium, Ethanoligenens, Megasphaera, Prevotella and Trichococcus with relative abundance of 2.1%∼28.1% were the dominant hydrogen-producing bacteria in C1. Methanogens (Methanothrix and Methanobacterium) dominated in the last three compartments. Function predicted analysis revealed that the abundance of metabolic-related gene families containing carbohydrate, amino acids and energy in the last three compartments were higher than that in C1. A deduced biodegradation model of CSPW in ABR revealed that the anaerobic sludge in C1 mainly produced hydrogen. Microbial population in C3 was responsible for COD removal and methane production. The redundancy analysis revealed that hydrogen production was highly correlated with some hydrogen-producing bacteria in C1, whereas methane production was positively correlated with microbial group in C2∼ C4.

Biopreservation of beer: Potential and constraints

The biopreservation of beer, using only antimicrobial agents of natural origin to ensure microbiological stability, is of great scientific and commercial interest. This review article highlights progress in the biological preservation of beer. It describes the antimicrobial properties of beer components and microbiological spoilage risks. It discusses novel biological methods for enhancing beer stability, using natural antimicrobials from microorganisms, plants, and animals to preserve beer, including legal restrictions. The future of beer preservation will involve the skilled knowledge-based exploitation of naturally occurring components in beer, supplementation with generally regarded as safe antimicrobial additives, and mild physical treatments.

Megasphaera lornae sp. nov., Megasphaera hutchinsoni sp. nov., and Megasphaera vaginalis sp. nov.: novel bacteria isolated from the female genital tract

Six strictly anaerobic Gram-negative bacteria representing three novel species were isolated from the female reproductive tract. The proposed type strains for each species were designated UPII 199-6^T, KA00182^T and BV3C16-1^T. Phylogenetic analyses based on 16S rRNA gene sequencing indicated that the bacterial isolates were members of the genus Megasphaera. UPII 199-6^T and KA00182^T had 16S rRNA gene sequence identities of 99.9 % with 16S rRNA clone sequences previously amplified from the human vagina designated as Megasphaera type 1 and Megasphaera type 2, members of the human vaginal microbiota associated with bacterial vaginosis, preterm birth and HIV acquisition. UPII 199-6^T exhibited sequence identities ranging from 92.9 to 93.6 % with validly named Megasphaera isolates and KA00182^T had 16S rRNA gene sequence identities ranging from 92.6-94.2 %. BV3C16-1^T was most closely related to Megasphaera cerevisiae with a 16S rRNA gene sequence identity of 95.4 %. Cells were coccoid or diplococcoid, non-motile and did not form spores. Genital tract isolates metabolized organic acids but were asaccharolytic. The isolates also metabolized amino acids. The DNA G+C content for the genome sequences of UPII 199-6^T, KA00182^T and BV3C16-1^T were 46.4, 38.9 and 49.8 mol%, respectively. Digital DNA-DNA hybridization and average nucleotide identity between the genital tract isolates and other validly named Megasphaera species suggest that each isolate type represents a new species. The major fatty acid methyl esters include the following: C_12 : 0, C_16 : 0, C_16 : 0 dimethyl acetal (DMA) and summed feature 5 (C_15 : 0 DMA and/or C_14 : 0 3-OH) in UPII 199-6^T; C_16 : 0 and C_16 : 1 cis 9 in KA00182^T; C_12 : 0; C_14 : 0 3-OH; and summed feature 5 in BV3C16-1^T. The isolates produced butyrate, isobutyrate, and isovalerate but there were specific differences including production of formate and propionate. Together, these data indicate that UPII 199-6^T, KA00182^T and BV3C16-1^T represent novel species within the genus Megasphaera. We propose the following names: Megasphaera lornae sp. nov. for UPII 199-6^T representing the type strain of this species (=DSM 111201^T=ATCC TSD-205^T), Megasphaera hutchinsoni sp. nov. for KA00182^T representing the type strain of this species (=DSM 111202^T=ATCC TSD-206^T) and Megasphaera vaginalis sp. nov. for BV3C16-1^T representing the type strain of this species (=DSM 111203^T=ATCC TSD-207^T).

Pectinatus spp. - Unpleasant and recurrent brewing spoilage bacteria

Traditionally, beer has been recognised as a beverage with high microbiological stability because of the hostile growth environment posed by beer and increasing attention being paid to brewery hygiene. However, the microbiological risk has increased in recent years because of technological advances toward reducing oxygen in beers, besides the increase in novel beer styles production, such as non-pasteurised, flash pasteurised, cold sterilised, mid-strength, and alcoholic-free beer, that are more prone to spoilage bacteria. Moreover, using innovative beer ingredients like fruits and vegetables is an added cause of microbial spoilage. To maintain quality and good brand image, beer spoilage microorganisms are a critical concern for breweries worldwide. Pectinatus and Megasphaera are Gram-negative bacteria mostly found in improper brewing environments, leading to consumer complaints and financial losses. Because of the lack of compiled scientific knowledge on Pectinatus spoilage ability, this review provides a comprehensive overview of the occurrence, survival mechanisms, and the factors affecting beer spoilage Pectinatus species in the brewing process.

Megasphaera vaginalis sp. nov. and Anaerococcus vaginimassiliensis sp. nov., new bacteria isolated from vagina of French woman with bacterial vaginosis

Using the culturomics method, two strains were isolated, identified and characterized following the taxonogenomics concept. Megasphaera vaginalis sp. nov. strain Marseille-P4512 (= CSURP4512) and Anaerococcus vaginimassiliensis sp. nov. strain Marseille-P4857 (= CSURP4857) were isolated from the vagina of a French woman. The phylogenic tree, phenotypic criteria and genomic analysis described here clearly show that these two bacteria are different from previously known bacterial species with standing in nomenclature and new members of Firmicutes phylum.

Comparative genetic and physiological characterisation of Pectinatus species reveals shared tolerance to beer-associated stressors but halotolerance specific to pickle-associated strains

Obligate anaerobic bacteria from the genus Pectinatus have been known to cause beer spoilage for over 40 years. Whole genome sequencing was performed on eleven beer spoilage strains (nine Pectinatus frisingensis, one Pectinatus cerevisiiphilus and one Pectinatus haikarae isolate), as well as two pickle spoilage species (Pectinatus brassicae MB591 and Pectinatus sottacetonis MB620) and the tolerance of all species to a range of environmental conditions was tested. Exploration of metabolic pathways for carbohydrates, amino acids and vitamins showed little difference between beer spoilage- and pickle spoilage-associated strains. However, genes for certain carbohydrate- and sulphur-containing amino acid-associated enzymes were only present in the beer spoilage group and genes for specific transporters and regulatory genes were uniquely found in the pickle spoilage group. Transporters for compatible solutes, only present in pickle-associated strains, likely explain their experimentally observed higher halotolerance compared to the beer spoilers. Genes involved in biofilm formation and ATP Binding Cassette (ABC) transporters potentially capable of exporting hop-derived antimicrobial compounds were found in all strains. All species grew in the presence of alcohol up to 5% alcohol by volume (ABV) and hops extract up to 80 ppm of iso-α-acids. Therefore, the species isolated from pickle processes may pose novel hazards in brewing.

Colibacter massiliensis gen. nov. sp. nov., a novel Gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon

The gut microbiota is considered to play a key role in human health. As a consequence, deciphering its microbial diversity is mandatory. A polyphasic taxonogenomic strategy based on the combination of phenotypic and genomic analyses was used to characterize a new bacterium, strain Marseille-P2911. This strain was isolated from a left colon sample of a 60-year old man who underwent a colonoscopy for an etiological investigation of iron-deficiency anemia in Marseille, France. On the basis of 16S rRNA sequence comparison, the closest phylogenetic neighbor was Anaeroglobus geminatus (94.59% 16S rRNA gene sequence similarity) within the family Veillonellaceae. Cells were anaerobic, Gram-stain-positive, non-spore-forming, catalase/oxidase negative cocci grouped in pairs. The bacterium was able to grow at 37 °C after 2 days of incubation. Strain Marseille-P2911 exhibited a genome size of 1,715,864-bp with a 50.2% G + C content, and digital DNA-DNA hybridization (dDDH) and OrthoANI values with A. geminatus of only 19.1 ± 4.5% and 74.42%, respectively. The latter value being lower than the threshold for genus delineation (80.5%), we propose the creation of the new genus Colibacter gen. nov., with strain Marseille-P2911^T (=DSM 103304 = CSUR P2911) being the type strain of the new species Colibacter massiliensis gen. nov., sp. nov.

Functional bacterial and archaeal dynamics dictated by pH stress during sugar refinery wastewater in a UASB

The operation performance and microbial mechanisms by pH stress were investigated during anaerobic digestion of sugar refinery wastewater in a upflow anaerobic sludge blanket (UASB) reactor to clarify correlations between pH stress, microbial community and process efficiency. Results showed that the COD removal and methane yield were respectively reduced by 24.8% and 25.3% as pH decreased to 5.0. pH decrease resulted in the composition of dominant fermentative acidogenic bacteria was changed to Butyricicoccus, Lactococcus, Brooklawnia, Armatimonadetes_gp2 and Megasphaera from Prevotella, Streptococcus, Acidaminococcus and Megasphaera, causing an increase in propionate production. In addition, the growth of propionate-oxidizing bacteria was also inhibited at pH 5.0, leading the propionate was accumulated, and then reduced the process efficiency. Methane was mainly produced through acetate cleavage by Methanosaeta during the whole operational period of UASB. pH decrease blocked the metabolic balance and community structure between different trophic groups, resulting in the decrease in reactor performance.

Megasphaera stantonii sp. nov., a butyrate-producing bacterium isolated from the cecum of a healthy chicken

A novel mesophilic, anaerobic, Gram-stain-negative bacterium was isolated from the cecum of a healthy white leghorn chicken, and designated AJH120^T. Cells were coccoid or diplococcoid with an average size of 0.8-1.8 µm and were non-motile with no evidence of spores. Phylogenetic analysis of 16S rRNA gene sequences revealed this organism to be a member of the genus Megasphaera, with the closest relatives being Megasphaera elsdenii (95 % sequence identity) and Megasphaera cerevisiae (95 % sequence identity). Growth was observed between 30 and 50 °C and between pH 5.0 and 9.0. AJH120^T utilized a variety of carbon sources, including succinate, gluconate, fructose, ribose and pyruvate, as well as many individual amino acids. The DNA G+C content for the genome sequence of AJH120^T was 52.1 mol%. Digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) between AJH120^T and close taxonomic relatives, indicated divergence consistent with the strain representing a novel species. The major fatty acid methyl esters of the organism were C12 : 0, C14 : 0 3-OH, C18 : 1ω9c, C16 : 0 and C16 : 1ω9c. AJH120^T was able to produce several short chain fatty acids, including butyrate, acetate, propionate and isovalerate. Together, these data indicate that AJH120^T represents a novel species within the genus Megasphaera. We propose the name Megasphaerastantonii sp. nov. for the species. The type strain of this species is AJH120^T (=DSM 106750^T=CCUG 71842^T).

Megasphaera hexanoica sp. nov., a medium-chain carboxylic acid-producing bacterium isolated from a cow rumen

Strain MHT, a strictly anaerobic, Gram-stain-negative, non-spore-forming, spherical coccus or coccoid-shaped microorganism, was isolated from a cow rumen during a screen for hexanoic acid-producing bacteria. The microorganism grew at 30-40 °C and pH 5.5-7.5 and exhibited production of various short- and medium-chain carboxylic acids (acetic acid, butyric acid, pentanoic acid, isobutyric acid, isovaleric acid, hexanoic acid, heptanoic acid and octanoic acid), as well as H2 and CO2 as biogas. Phylogenetic analysis based on 16S rRNA gene sequencing demonstrated that MHT represents a member of the genus Megasphaera, with the closest relatives being Megapsphaera indica NMBHI-10T (94.1 % 16S rRNA sequence similarity), Megasphaera elsdenii DSM 20460T (93.8 %) and Megasphaera paucivorans DSM 16981T (93.8 %). The major cellular fatty acids produced by MHT included C12 : 0, C16 : 0, C18 : 1cis 9, and C18 : 0, and the DNA G+C content of the MHT genome is 51.8 mol%. Together, the distinctive phenotypic and phylogenetic characteristics of MHT indicate that this microorganism represents a novel species of the genus Megasphaera, for which the name Megasphaera hexanoica sp. nov. is herein proposed. The type strain of this species is MHT (=KCCM 43214T=JCM 31403T).

Biochemical and genome sequence analyses of Megasphaera sp. strain DISK18 from dental plaque of a healthy individual reveals commensal lifestyle

Much of the work in periodontal microbiology in recent years has focused on identifying and understanding periodontal pathogens. As the majority of oral microbes have not yet been isolated in pure form, it is essential to understand the phenotypic characteristics of microbes to decipher their role in oral environment. In this study, strain DISK18 was isolated from gingival sulcus and identified as a Megasphaera species. Although metagenomics studies revealed Megasphaera species as a major group within the oral habitat, they have never been isolated in cultivable form to date. Therefore, we have characterized the DISK18 strain to better understand its role in the periodontal ecosystem. Strain Megasphaera sp. DISK18 displayed the ability to adhere and self-aggregate, which are essential requisite features for inhabiting and persisting in oral cavity. It also coaggregated with other pioneer oral colonizers like Streptococcus and Lactobacillus species but not with Veillonella. This behaviour points towards its role in the ecologic succession of a multispecies biofilm as an early colonizer. The absence of virulence determining genes as observed in whole genome sequence analysis coupled with an inability to degrade collagen reveals that Megasphaera sp. strain DISK18 is likely not a pathogenic species and emphasizes its commensal lifestyle.

Microbial Diversity and Biochemical Analysis of Suanzhou: A Traditional Chinese Fermented Cereal Gruel

Suanzhou as a traditional Chinese gruel is fermented from proso millet and millet. The biochemical analysis showed Suanzhou had relatively high concentrations of lactic acid, acetic acid, and free amino acids. The metagenomics of Suanzhou were studied, with the analysis of the V4 region of 16S rRNA gene, the genera Lactobacillus and Acetobacter were found dominant with the average abundance of 58.2 and 24.4%, respectively; and with the analysis of the ITS1 region between 18S and 5.8S rRNA genes, 97.3% of the fungal community was found belonging to the genus Pichia and 2.7% belonging to five other genera. Moreover, the isolates recovered from 59 Suanzhou samples with various media were identified with the 16S rRNA or 18S rRNA gene analyses. Lactobacillus fermentum (26.9%), L. pentosus (19.4%), L. casei (17.9%), and L. brevis (16.4%) were the four dominant Lactobacillus species; Acetobacter lovaniensis (38.1%), A. syzygii (16.7%), A. okinawensis (16.7%), and A. indonesiensis (11.9%) were the four dominant Acetobacter species; and Pichia kudriavzevii (55.8%) and Galactomyces geotrichum (23.1%) were the two dominant fungal species. Additionally, L. pentosus p28-c and L. casei h28-c1 were selected for the fermentations mimicking the natural process. Collectively, our data demonstrate that Suanzhou is a nutritional food high in free amino acids and organic acids. Diverse Lactobacillus, Acetobacter, and yeast species are identified as the dominant microorganisms in Suanzhou. The isolated strains can be further characterized and used as starters for the industrial production of Suanzhou safely.

Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods

Fermented cucumber spoilage (FCS) characterized by rising pH and the appearance of manure- and cheese-like aromas is a challenge of significant economical impact for the pickling industry. Previous culture-based studies identified the yeasts Pichia manshurica and Issatchenkia occidentalis, 4 Gram-positive bacteria, Lactobacillus buchneri, Lactobacillus parrafaraginis, Clostridium sp., and Propionibacterium and 1 Gram-negative genus, Pectinatus, as relevant in various stages of FCS given their ability to metabolize lactic acid. It was the objective of this study to augment the current knowledge of FCS using culture-independent methods to microbiologically characterize commercial spoilage samples. Ion Torrent data and 16S rRNA cloning library analyses of samples collected from commercial fermentation tanks confirmed the presence of L. rapi and L. buchneri and revealed the presence of additional species involved in the development of FCS such as Lactobacillus namurensis, Lactobacillus acetotolerans, Lactobacillus panis, Acetobacter peroxydans, Acetobacter aceti, and Acetobacter pasteurianus at pH below 3.4. The culture-independent analyses also revealed the presence of species of Veillonella and Dialister in spoilage samples with pH above 4.0 and confirmed the presence of Pectinatus spp. during lactic acid degradation at the higher pH. Acetobacter spp. were successfully isolated from commercial samples collected from tanks subjected to air purging by plating on Mannitol Yeast Peptone agar. In contrast, Lactobacillus spp. were primarily identified in samples of FCS collected from tanks not subjected to air purging for more than 4 mo. Thus, it is speculated that oxygen availability may be a determining factor in the initiation of spoilage and the leading microbiota.

The use of the carbon/nitrogen ratio and specific organic loading rate as tools for improving biohydrogen production in fixed-bed reactors

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The effects of the carbon/nitrogen ratios of 40, 90, 140, and 190 on hydrogen production are evaluated by varying the nitrogen source in an upflow fixed-bed anaerobic reactor.

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An optimal C/N ratio of 137 to produce 3.5 mol H₂ mol⁻¹ sucrose is estimated by a mathematical approximation.

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Continuous decreases in the specific organic loading rate as a function of time seemed to be responsible for the instability of the system.

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A microbial biology analysis identified hydrogen-producing and -consuming microorganisms from natural inoculum.

This study assessed the effect of the carbon/nitrogen (C/N) ratio on the hydrogen production from sucrose-based synthetic wastewater in upflow fixed-bed anaerobic reactors. C/N ratios of 40, 90, 140, and 190 (g C/g N) were studied using sucrose and urea as the carbon and nitrogen sources, respectively. An optimum hydrogen yield of 3.5 mol H₂ mol⁻¹ sucrose was obtained for a C/N ratio of 137 by means of mathematical adjustment. For all C/N ratios, the sucrose removal efficiency reached values greater than 80% and was stable after the transient stage. However, biogas production was not stable at all C/N ratios as a consequence of the continuous decreasing of the specific organic loading rate (SOLR) when the biomass accumulated in the fixed-bed, causing the proliferation of H₂-consuming microorganisms. It was found that the application of a constant SOLR of 6.0 g sucrose g⁻¹ VSS d⁻¹ stabilized the system.

Development of a species-specific PCR assay for identification of the strictly anaerobic bacterium Selenomonas lacticifex found in biofilm-covered surfaces in brewery bottling halls

AIMS

In recent years, beer-spoilage cases from strictly anaerobic bacteria have risen in frequency, in connection with the production of non-pasteurized, non-alcohol and low-alcoholic beers and with the lowering of dissolved oxygen in the packaged beer. Selenomonas lacticifex, found in brewer's yeast and in biofilms covering some surfaces in brewery bottling area, is considered to be a beer-spoilage organism. This study aims to develop S. lacticifex-specific PCR assay. The objective of this study was also evaluation of the specificity and reproducibility of the developed PCR assay in real brewery samples.

METHODS AND RESULTS

Three primers (one forward and two reverse) were designed for identification of the strictly anaerobic bacterium S. lacticifex on the basis of the species-specific sequences of the 16S rDNA region. The specificity of the primers was tested against 44 brewery-related non-target micro-organisms that could potentially occur in the same brewery specimens. None of the primer pairs amplified DNA from any of the non-S. lacticifex strains tested including genera from the same family (Pectinatus, Megasphaera, Zymophilus) and the closely related species Selenomonas ruminantium, showing thus 100% specificity.

CONCLUSIONS

The PCR assay developed in this study enables the detection of the strictly anaerobic bacterium S. lacticifex in real brewery samples including pitching yeast.

SIGNIFICANCE AND IMPACT OF THE STUDY

Selenomonas lacticifex-specific PCR assay developed in this study allows for the extension of the spectra of detected beer-spoilage micro-organisms in brewing laboratories and thus lowering the risk of contamination of the final product.

Megasphaera indica sp. nov., an obligate anaerobic bacteria isolated from human faeces

Two coccoid, non-motile, obligately anaerobic, Gram-stain-negative bacteria, occurring singly or in pairs, or as short chains, with a mean size of 1.4-2.5 µm were isolated from the faeces of two healthy human volunteers, aged 26 and 56 years, and were designated NMBHI-10(T) and BLPYG-7, respectively. Both the strains were affiliated to the sub-branch Sporomusa of the class Clostridia as revealed by 16S rRNA gene sequence analysis. The isolates NMBHI-10(T) and BLPYG-7 showed 99.1 and 99.2% 16S rRNA gene sequence similarity, respectively, with Megasphaera elsdenii JCM 1772(T). DNA-DNA hybridization and phenotypic analysis showed that both the strains were distinct from their closest relative, M. elsdenii JCM 1772(T) (42 and 53% DNA-DNA relatedness with NMBHI-10(T) and BLPYG-7, respectively), but belong to the same species (DNA-DNA relatedness of 80.9 % between the isolates). According to DNA-DNA hybridization results, the coccoid strains belong to the same genospecies, and neither is related to any of the recognized species of the genus Megasphaera. Strains NMBHI-10(T) and BLPYG-7 grew in PYG broth at temperatures of between 15 and 40 °C (optimum 37 °C), but not at 45 °C. The strains utilized a range of carbohydrates as sources of carbon and energy including glucose, lactose, cellobiose, rhamnose, galactose and sucrose. Glucose fermentation resulted in the formation of volatile fatty acids, mainly caproic acid and organic acids such as succinic acid. Phylogenetic analysis, specific phenotypic characteristics and/or DNA G+C content also differentiated the strains from each other and from their closest relatives. The DNA G+C contents of strains NMBHI-10(T) and BLPYG-7 are 57.7 and 54.9 mol%, respectively. The major fatty acids were 12 : 0 FAME and 17 : 0 CYC FAME. On the basis of these data, we conclude that strains NMBHI-10(T) and BLPYG-7 should be classified as representing a novel species of the genus Megasphaera, for which the name Megsphaera indica sp. nov. is proposed. The type strain is NMBHI-10(T) ( = DSM 25563(T) = MCC 2481(T)).

Bacterial community structure in maximum volatile fatty acids production from alginate in acidogenesis

Alginate as biomass feedstock for bioconversion into volatile fatty acids (VFAs) is limited primarily by the low solubility in water or little utilization as microbial substrate and yet unknown about the microbial community structure for acidogenesis. The bacterial community structure was demonstrated the reflected changes in VFAs profiles in the maximized acidogenic process from alginate. Bacteroides- and Clostridium-related microorganisms were suggested to be mainly responsible for the hydrolysis of alginate and VFAs production, respectively. And the bacterial community shifted corresponded to VFAs producing was statistically demonstrated. A number of features discussed in this research can stimulate further interests on bioconversion of alginate into anaerobic biofuels production.

Comparative genome analysis of Megasphaera sp. reveals niche specialization and its potential role in the human gut

With increasing number of novel bacteria being isolated from the human gut ecosystem, there is a greater need to study their role in the gut ecosystem and their effect on the host health. In the present study, we carried out in silico genome-wide analysis of two novel Megasphaera sp. isolates NM10 (DSM25563) and BL7 (DSM25562), isolated from feces of two healthy individuals and validated the key features by in vitro studies. The analysis revealed the general metabolic potential, adaptive features and the potential effects of these isolates on the host. The comparative genome analysis of the two human gut isolates NM10 and BL7 with ruminal isolate Megasphaera elsdenii (DSM20460) highlighted the differential adaptive features for their survival in human gut. The key findings include features like bile resistance, presence of various sensory and regulatory systems, stress response systems, membrane transporters and resistance to antibiotics. Comparison of the “glycobiome” based on the genomes of the ruminal isolate with the human gut isolates NM10 and BL revealed the presence of diverse and unique sets of Carbohydrate-Active enzymes (CAZymes) amongst these isolates, with a higher collection of CAZymes in the human gut isolates. This could be attributed to the difference in host diet and thereby the environment, consequently suggesting host specific adaptation in these isolates. In silico analysis of metabolic potential predicted the ability of these isolates to produce important metabolites like short chain fatty acids (butyrate, acetate, formate, and caproate), vitamins and essential amino acids, which was further validated by in vitro experiments. The ability of these isolates to produce important metabolites advocates for a potential healthy influence on the host. Further in vivo studies including transcriptomic and proteomic analysis will be required for better understanding the role and impact of these Megasphaera sp. isolates NM10 and BL7 on the human host.

Pectinatus sottacetonis sp. nov., isolated from a commercial pickle spoilage tank

A strictly anaerobic, Gram-stain-negative, non-spore-forming, motile bacterium, designated strain FSRU B0405T, was isolated from a commercial pickle spoilage tank and characterized by biochemical, physiological and molecular biological methods. Analyses of the 16S rRNA gene sequence of strain FSRU B0405T showed affiliation to the class Negativicutes in the phylum Firmicutes , with the closest relatives being the type strains of Pectinatus haikarae (96 %) and Pectinatus brassicae (95 %). In maximum-likelihood and neighbour-joining phylogenetic trees, strain FSRU B0405T clustered definitively (in 100 % of bootstrapped trees) within the genus Pectinatus , but not specifically with any characterized species within this genus. Strain FSRU B0405T was a slightly curved rod, varying from 3 to 30 µm in length, motile with a distinctive X-wise movement, having flagella only on the concave side of the cell. The isolate produced acetate and propionate from fructose and glucose as major metabolites similar to type strains of species of the genus Pectinatus . The major fatty acids were C11 : 0, C13 : 0, C15 : 0, C13 : 0 3-OH, C17 : 1 and C18 : 1ω11t. Strain FSRU B0405T differed from the pickle wastewater strain, Pectinatus brassicae TYT, due to its lack of susceptibility to vancomycin, acetoin production, growth temperature range, acid production from adonitol, erythritol, glycerol, inositol, lactose, maltose, mannose, ribose, salicin, sorbitol, trehalose and xylitol and lack of hydrolysis of milk. Strain FSRU B0405T could be differentiated from other species of the genus Pectinatus both phenotypically and genetically. The results indicate that strain FSRU B0405T represents a novel species of the genus Pectinatus , for which the name Pectinatus sottacetonis sp. nov. is proposed. The type strain is FSRU B0405T ( = ATCC BAA-2501T = VTT E-113163T). An emended description of the genus Pectinatus is also provided.

Characterization of cucumber fermentation spoilage bacteria by enrichment culture and 16S rDNA cloning

Commercial cucumber fermentations are typically carried out in 40000 L fermentation tanks. A secondary fermentation can occur after sugars are consumed that results in the formation of acetic, propionic, and butyric acids, concomitantly with the loss of lactic acid and an increase in pH. Spoilage fermentations can result in significant economic loss for industrial producers. The microbiota that result in spoilage remain incompletely defined. Previous studies have implicated yeasts, lactic acid bacteria, enterobacteriaceae, and Clostridia as having a role in spoilage fermentations. We report that Propionibacterium and Pectinatus isolates from cucumber fermentation spoilage converted lactic acid to propionic acid, increasing pH. The analysis of 16S rDNA cloning libraries confirmed and expanded the knowledge gained from previous studies using classical microbiological methods. Our data show that Gram-negative anaerobic bacteria supersede Gram-positive Fermincutes species after the pH rises from around 3.2 to pH 5, and propionic and butyric acids are produced. Characterization of the spoilage microbiota is an important first step in efforts to prevent cucumber fermentation spoilage.

PRACTICAL APPLICATION

An understanding of the microorganisms that cause commercial cucumber fermentation spoilage may aid in developing methods to prevent the spoilage from occurring.

Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov

Megasphaera massiliensis strain NP3(T) sp. nov. is the type strain of Megasphaera massiliensis sp. nov., a new species within the genus Megasphaera. This strain, whose genome is described here, was isolated from the fecal flora of an HIV-infected patient. M. massiliensis is a Gram-negative, obligate anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,661,757 bp long genome (1 chromosome but no plasmid) contains 2,577 protein-coding and 61 RNA genes, including 5 rRNA genes.

The microbiology of malting and brewing

Brewing beer involves microbial activity at every stage, from raw material production and malting to stability in the package. Most of these activities are desirable, as beer is the result of a traditional food fermentation, but others represent threats to the quality of the final product and must be controlled actively through careful management, the daily task of maltsters and brewers globally. This review collates current knowledge relevant to the biology of brewing yeast, fermentation management, and the microbial ecology of beer and brewing.

Pectinatus brassicae sp. nov., a Gram-negative, anaerobic bacterium isolated from salty wastewater

A novel Gram-negative, non-spore-forming, strictly anaerobic, heterotrophic bacterium, strain TYT, was isolated from salty pickle wastewater. Cells were rod-shaped with comb-like flagella, slightly curved and very variable in length. Optimal growth occurred at 28 °C and pH 6.5. Cells were resistant to up to 50 g NaCl l−1. Strain TYT produced acid from glycerol, sucrose, glucose, fructose and mannitol. The main fermentation products from glucose were acetic and propionic acids. Tests for acid phosphatase and naphthol-AS-BI-phosphohydrolase activities were positive. The major fatty acids were C14 : 0 DMA (18.7 %), C15 : 0 (15.4 %), anteiso-C18 : 1 (15.2 %), C11 : 0 (13.3 %) and summed feature 5 (C17 : 1ω7c and/or C17 : 2) (11.0 %). The DNA G+C content was 35.9 mol%. 16S rRNA gene sequence-based phylogenetic analysis indicated that strain TYT represented a novel species of the genus Pectinatus (sequence similarity to other members of the genus ranged from 93.2 to 94.8 %). Based on its phenotypic, genotypic and phylogenetic characteristics, strain TYT is proposed to represent a novel species, named Pectinatus brassicae sp. nov. (type strain TYT  = JCM 17499T  = DSM 24661T).

Development of a 16S rRNA gene primer and PCR-restriction fragment length polymorphism method for rapid detection of members of the genus Megasphaera and species-level identification

The genus Megasphaera is relevant to the environment, human health and food, and renewable energy for the future. In this study, a primer set was designed for PCR-restriction fragment length polymorphism (RFLP) analyses to detect and identify the members of Megasphaera. Direct detection and identification were achieved for environmental samples and isolates.

Bioprotective potential of lactic acid bacteria in malting and brewing

Lactic acid bacteria (LAB) are naturally associated with many foods or their raw ingredients and are popularly used in food fermentation to enhance the sensory, aromatic, and textural properties of food. These microorganisms are well recognized for their biopreservative properties, which are achieved through the production of antimicrobial compounds such as lactic acid, diacetyl, bacteriocins, and other metabolites. The antifungal activity of certain LAB is less well characterized, but organic acids, as yet uncharacterized proteinaceous compounds, and cyclic dipeptides can inhibit the growth of some fungi. A variety of microbes are carried on raw materials used in beer brewing, rendering the process susceptible to contamination and often resulting in spoilage or inferior quality of the finished product. The application of antimicrobial-producing LAB at various points in the malting and brewing process could help to negate this problem, providing an added hurdle for spoilage organisms to overcome and leading to the production of a higher quality beer. This review outlines the bioprotective potential of LAB and its application with specific reference to the brewing industry.

Group-specific PCR-RFLP and real-time PCR methods for detection and tentative discrimination of strictly anaerobic beer-spoilage bacteria of the class Clostridia

The strictly anaerobic brewery contaminants of the genera Pectinatus, Megasphaera, Selenomonas and Zymophilus in the class Clostridia constitute an important group of spoilage bacteria of unpasteurised, packaged beers. The aim of this study was to develop and evaluate group-specific PCR methods to detect and differentiate these bacteria in beer. A group-specific primer pair targeting a 342-bp variable region of the 16S rRNA gene was designed and evaluated in end-point PCR with gel electrophoresis and in real-time PCR with SYBR Green I dye. Significant cross-reactions with DNAs from any of the forty-two brewery-related, non-target microbes or from real brewery samples were not detected in either PCR system. The group-specific end-point and real-time PCR products could be differentiated according to species/genus and spoilage potential using restriction fragment length polymorphism (KpnI, XmnI, BssHII, ScaI) and melting point curve analysis, respectively. In combination with a rapid DNA extraction method, the PCR reactions detected ca 10(0)-10(3) CFU per 25 ml of beer depending on the strain and on the PCR system. The end-point and real-time PCR analysis took 6-7 h and 2-3 h, respectively. Pre-PCR enrichment of beer samples for 1-3 days ensured the detection of even a single cultivable cell. The PCR and cultivation results of real brewery samples were mostly congruent but the PCR methods were occasionally more sensitive. The PCR methods developed allow the detection of all the nine beer-spoilage Pectinatus, Megasphaera, Selenomonas and Zymophilus species in a single reaction and their differentiation below group level and reduce the analysis time for testing of their presence in beer samples by 1-2 days. The methods can be applied for brewery routine quality control and for studying occurrence, diversity and numbers of the strictly anaerobic beer spoilers in the brewing process.