The Sporobiota of the Human Gut

The human gut microbiome is a diverse and complex ecosystem that plays a critical role in health and disease. The composition of the gut microbiome has been well studied across all stages of life. In recent years, studies have investigated the production of endospores by specific members of the gut microbiome. An endospore is a tough, dormant structure formed by members of the Firmicutes phylum, which allows for greater resistance to otherwise inhospitable conditions. This innate resistance has consequences for human health and disease, as well as in biotechnology. In particular, the formation of endospores is strongly linked to antibiotic resistance and the spread of antibiotic resistance genes, also known as the resistome. The term sporobiota has been used to define the spore-forming cohort of a microbial community. In this review, we present an overview of the current knowledge of the sporobiota in the human gut. We discuss the development of the sporobiota in the infant gut and the perinatal factors that may have an effect on vertical transmission from mother to infant. Finally, we examine the sporobiota of critically important food sources for the developing infant, breast milk and powdered infant formula.

Pilot-scale investigation of sludge reduction in aerobic digestion system with endospore-forming bacteria

A pilot-scale investigation of membrane-based aerobic digestion system dominated by endospore-forming bacteria was evaluated as one of the potential sludge treatment processes (STP). Most of the organic matter in the sludge was removed (90.1%) by the particular bacteria in the STP, which consisted of mixed liquor suspended solid (MLSS) contact reactor (MCR), MLSS oxidation reactor (MOR), and membrane bioreactor (MBR). The sludge was accumulated in the MBR without wasting, and then the effluent in STP was fed into the first step in water resource recovery facility (WRRF). According to the analysis of microbial communities in all reactors, various Bacillus species were present in the STP, mainly due to their intrinsic resistance to the extreme conditions. As the surviving Bacillus species might consume degraded microorganisms for their growth, these endospore-forming bacteria-based STP could be suitable for the sludge reduction when they operated for a long time.

Electron microscopic examination of the dormant spore and the sporulation of Paenibacillus motobuensis strain MC10

We previously reported a new species Paenibacillus motobuensis. The type strain MC10 was stained gram-negative, but had a gram-positive cell wall structure and its spore had a characteristic star shape. The spore and sporulation process of P. motobuensis strain MC10 were examined by electron microscopy using the technique of freeze-substitution in thin sectioning. The structure of the dormant spore was basically the same as that of the other Bacillus spp. The core of the spore was enveloped with two main spore components, the cortex and the spore coat. In thin section, the spore showed a star-shaped image, which was derived from the structure of the spore coat, which is composed of three layers, namely the inner, middle and outer spore coat. The middle coat was an electron-dense thick layer and had a characteristic ridge. By scanning electron microscopic observation, the ridges were seen running parallel to the long axis of the oval-shaped spore. The process of sporulation was essentially the same as that of the other Bacillus spp. The forespore was engulfed by the mother cell membrane, then the spore coat and the cortex were accumulated in the space between the mother cell membrane and forespore membrane. The mother cell membrane seemed to participate in the synthesis of the spore coat. MC10 strain showed almost identical heat resistance to that of B. subtilis.

Genetic and physiological regulation of bacterial endospore development

Bacterial endospores are complex structures residing inside endospore-forming, mainly gram-positive bacteria. The process of sporulation is considered a simple example of cell differentiation. Endospores enable the organism to resist environmental stresses. Sporulation can be divided into several stages, from axial DNA filamentation to mother cell lysis. The structure and formation of an endospore is an attractive model for the assembly of complex macromolecular structures during development. The expression of genes involved in sporulation is compartmentalized and different sets of genes are expressed in the prespore and mother cell, this being associated with the subsequent activation of four sporulation-specific sigma factors. Their synthesis and activity are tightly regulated and the regulatory mechanisms have overlapping roles.

Paenibacillus sepulcri sp. nov., isolated from biodeteriorated mural paintings in the Servilia tomb

In 2001, a Gram-variable, facultatively anaerobic, endospore-forming bacterium isolated from biodeteriorated mural paintings in the Servilia tomb of the Roman necropolis of Carmona was deposited as Paenibacillus strain LMG 19508. Subsequently, the strain was characterized in detail using phenotypic and molecular methods. The 16S rRNA gene sequence confirmed that the strain belongs to the genus Paenibacillus and indicated its relationship to Paenibacillus mendelii CCM 4839(T) (96.7 % sequence similarity). The predominant menaquinone was MK-7. The cell wall contained meso-diaminopimelic acid of the A1gamma type. The DNA G+C content (50 mol%) and the major fatty acid (anteiso-C(15 : 0)) of strain LMG 19508(T) were also consistent with its affiliation to the genus Paenibacillus. DNA-DNA hybridization distinguished strain LMG 19508(T) from other phylogenetically related Paenibacillus species. Therefore, the isolate represents a novel species, for which the name Paenibacillus sepulcri sp. nov. is proposed. The type strain is CCM 7311(T) (=LMG 19508(T)).

Cellular Biophysics: Bacterial Endospore, Membranes and Random Fluctuation

Purposeful motion of biological processes can be driven by Brownian motion of macromolecular complexes with one-sided binding biasing movement in one direction: a Brownian ratchet, now proposed to explain membrane motion during a phagocytosis-like process in bacteria.

Effective terminal sterilization using supercritical carbon dioxide

Gentle alternatives to existing sterilization methods are called for by rapid advances in biomedical technologies. Supercritical fluid technologies have found applications in a wide range of areas and have been explored for use in the inactivation of medical contaminants. In particular, supercritical CO(2) is appealing for sterilization due to the ease at which the supercritical state is attained, the non-reactive nature, and the ability to readily penetrate substrates. However, rapid inactivation of bacterial endospores has proven a barrier to the use of this technology for effective terminal sterilization. We report the development of a supercritical CO(2) based sterilization process capable of achieving rapid inactivation of bacterial endospores while in terminal packaging. Moreover, this process is gentle; as the morphology, ultrastructure, and protein profiles of inactivated microbes are maintained. These properties of the sterilization process suit it for possible use on a wide range of biomedical products including: materials derived from animal tissues, protein based therapies, and other sensitive medical products requiring gentle terminal sterilization.

Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa

Earthworms emit nitrous oxide (N(2)O) via the activity of bacteria in their gut. Four N(2)O-producing facultative aerobes, ED1(T), ED5(T), MH21(T) and MH72, were isolated from the gut of the earthworm Aporrectodea caliginosa. The isolates produced N(2)O under conditions that simulated the microenvironment of the earthworm gut. ED1(T) and ED5(T) were Gram-negative, motile rods that carried out complete denitrification (i.e. the reduction of nitrate to N(2)) and contained membranous c-type cytochromes. ED1(T) grew optimally at 30 degrees C and pH 7. ED1(T) oxidized organic acids and reduced (per)chlorate, sulfate, nitrate and nitrite. The closest phylogenetic relative of ED1(T) was Dechloromonas agitata. ED5(T) grew optimally at 25 degrees C and pH 7. ED5(T) grew mainly on sugars, and nitrate and nitrite were used as alternative electron acceptors. The closest phylogenetic relatives of ED5(T) were Flavobacterium johnsoniae and Flavobacterium flevense. MH21(T) and MH72 were motile, spore-forming, rod-shaped bacteria with a three-layered cell wall. Sugars supported the growth of MH21(T) and MH72. Cells of MH21(T) grew in chains, were linked by connecting filaments and contained membranous b-type cytochromes. MH21(T) grew optimally at 30-35 degrees C and pH 7.7, grew by fermentation and reduced low amounts of nitrite to N(2)O. The closest phylogenetic relatives of MH21(T) were Paenibacillus borealis and Paenibacillus chibensis. Based on morphological, physiological and phylogenetic characteristics, ED1(T) (= DSM 15892(T) = ATCC BAA-841(T)), ED5(T) (= DSM 15936(T) = ATCC BAA-842(T)) and MH21(T) (=DSM 15890(T) = ATCC BAA-844(T)) are proposed as type strains of the novel species Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov. and Paenibacillus anaericanus sp. nov., respectively. MH72 is considered a new strain of Paenibacillus terrae.

Specificity of association between Paenibacillus spp. and the entomopathogenic nematodes, Heterorhabditis spp

Endospore-forming bacteria, Paenibacillus spp., have recently been isolated in association with insect pathogenic nematodes Heterorhabditis spp. Sporangia adhere to nematode infective juveniles (J3) and are carried with them into insects. Paenibacillus proliferates in the killed insect along with Heterorhabditis and its obligate bacterial symbiont, Photorhabdus, despite the antibiotic production of the latter. Nematode infective juveniles leave the insect cadaver with Paenibacillus sporangia attached. The specificity of the relationship between Paenibacillus and Heterorhabditis was investigated. Sporangia of nematode-associated Paenibacillus adhered to infective juveniles (but not other stages) of all Heterorhabditis species tested, and to infective juveniles of vertebrate parasitic Strongylida species, but not to a variety of other soil nematodes tested. Paenibacillus species that were not isolated from nematodes, but were phylogenetically close to the nematode-associated strains, did not adhere to Heterorhabditis, and they were also sensitive to Photorhabdus antibiotics in vitro, whereas the nematode-associated strains were not. Unusual longevity of the sporangium and resistance to Photorhabdus antibiotics may represent specific adaptations of the nematode-associated Paenibacillus strains to allow them to coexist with and be transported by Heterorhabditis. Adaptation to specific Heterorhabditis-Photorhabdus strains is evident among the three nematode-associated Paenibacillus strains (each from a different nematode strain). Paenibacillus NEM1a and NEM3 each developed best in cadavers with the nematode from which it was isolated and not at all with the nematode associate of the other strain. Differences between nematode-associated Paenibacillus strains in cross-compatibility with the various Heterorhabditis strains in cadavers could not be explained by differential sensitivity to antibiotics produced by the nematodes' Photorhabdus symbionts in vitro.

Isolation, characterization, and identification of bacterial contaminants in semifinal gelatin extracts

Bacterial contamination of gelatin is of great concern. Indeed, this animal colloid has many industrial applications, mainly in food and pharmaceutical products. In a previous study (E. De Clerck and P. De Vos, Syst. Appl. Microbiol. 25:611-618), contamination of a gelatin production process with a variety of gram-positive and gram-negative bacteria was demonstrated. In this study, bacterial contamination of semifinal gelatin extracts from several production plants was examined. Since these extracts are subjected to harsh conditions during production and a final ultrahigh-temperature treatment, the bacterial load at this stage is expected to be greatly reduced. In total, 1,129 isolates were obtained from a total of 73 gelatin batches originating from six different production plants. Each of these batches was suspected of having bacterial contamination based on quality control testing at the production plant from which it originated. For characterization and identification of the 1,129 bacterial isolates, repetitive-element PCR was used to obtain manageable groups. Representative strains were identified by means of 16S rRNA gene sequencing, species-specific gyrB PCR, and gyrA and rpoB sequencing and were tested for gelatinase activity. The majority of isolates belonged to members of Bacillus or related endospore-forming genera. Representative strains were identified as Bacillus cereus, Bacillus coagulans, Bacillus fumarioli, Bacillus amyloliquefaciens, Bacillus licheniformis, Bacillus pumilus, Bacillus sonorensis, Bacillus subtilis, Bacillus gelatini, Bacillus thermoamylovorans, Anoxybacillus contaminans, Anoxybacillus flavithermus, Brevibacillus agri, Brevibacillus borstelensis, and Geobacillus stearothermophilus. The majority of these species include strains exhibiting gelatinase activity. Moreover, some of these species have known pathogenic properties. These findings are of great concern with regard to the safety and quality of gelatin and its applications.

Alicyclobacillus acidoterrestris spores as a target for Cupuaçu (Theobroma grandiflorum) nectar thermal processing: kinetic parameters and experimental methods

The kinetic parameters of thermal inactivation of a spore former, Alicyclobacillus acidoterrestris, in a tropical fruit nectar [25% of Cupuaçu (Theobroma grandiflorum) pulp and 15% sugar] were determined by the isothermal method (IM), under batch heating, and by the paired equivalent isothermal exposures (PEIE) method, under non-isothermal continuous conditions. The isothermal experiments were repeated three times, every 4 months, with the same spore suspension kept frozen between experiments. The aging of spores, under frozen storage, seemed to produce a notorious increase in the z-value from experiment to experiment: Experiment 1 (z = 7.8 +/- 2.6 degrees C, D(95 degrees C) = 5.29 +/- 0.96 min), Experiment 2 (z = 22 +/- 5 degrees C, D(95 degrees C) = 5.99 +/- 0.63 min), and Experiment 3 (z =29 +/- 10 degrees C, D(95 degrees C) = 3.82 +/- 0.48 min). The evaluation of the kinetic parameters by the PEIE method was carried out in parallel with Experiment 3, with the same aged spores, and the results (z = 31 +/- 6 degrees C, D(95 degrees C) = 5.5 +/- 1.2 min) were close to the ones obtained in this experiment. From this work, it seems that the PEIE method can also be applied to evaluate the reduction parameters of a spore-forming microorganism, and in a more realistic way, since the continuous system eliminates the errors caused by come-up and cool-down times (CUT and CDT) that are unavoidable in isothermal experiments. Therefore, when designing a thermal process for a continuous system, the PEIE method should be used, or the chances are that the process would be underdesigned, risking that the desired level of spore inactivation would not be achieved. An optimization of the thermal processing conditions was next performed for Cupuaçu nectar, considering a 5D reduction in A. acidoterrestris spores. If a pasteurization process is considered, the conditions that ensure safety (9 min at 98 degrees C) only allow a 55% retention of ascorbic acid (AA). If sterilization is considered, 8 s at 115 degrees C will ensure a safe product and retain 98.5% of the original ascorbic acid. Therefore, if A. acidoterrestris is considered as the target microorganism, the nectar should undergo an aseptic high temperature short time principle (HTST) process to achieve a 5D reduction in this acidophilus spore former. However, if the hot-fill-and-hold pasteurization process is preferred, the product should be fortified with ascorbic acid.

[Geobacillus uralicus, a new species of thermophilic bacteria]

The K2T strain of thermophilic spore-forming bacteria was isolated from a biofilm on the surface of a corroded pipeline in an extremely deep well (4680 m, 40-72 degrees C) in the Ural. The cells are rod-shaped, motile, gram-variable. They grow on a complex medium with tryptone and yeast extract and on a synthetic medium with glucose and mineral salts without additional growth factors. The cells use a wide range of organic substances as carbon and energy sources. They exhibit a respiratory metabolism but are also capable of anaerobic growth on a nitrate-containing medium and of fermentation. Growth occurs within the 40-75 degrees C temperature range (with an optimum of 65 degrees C) and at pH 5-9. The minimum generation time (15 min) was observed at pH 7.5. Ammonium salts and nitrates are used as nitrogen sources. The G + C content of the DNA is 54.5 mol%. From the morphological, physiological, and biochemical properties and the nucleotide sequence of the 16S rRNA gene, it was concluded that the isolate K2T represents a new species of the genus Geobacillus, Geobacillus uralicus.

Paenibacillus jamilae sp. nov., an exopolysaccharide-producing bacterium able to grow in olive-mill wastewater

Endospore-forming strains were isolated from corn-compost treated with olive-mill wastewater ('alpechin'). The strains were taxonomically studied and proposed as a novel Paenibacillus species. These organisms (strains B.3T, B.7 and B.9) were particularly distinguishable from other aerobic spore-forming species by their ability to grow optimally in 100% (v/v) olive-mill wastewater at 30 degrees C and pH 7.0 and concomitant production of an interesting exopolysaccharide. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone, the major fatty acid was anteiso C15:0 and the cell wall contained meso-diaminopimelic acid. The DNA G+C content was 40.7 mol%. Comparative sequence analysis of 16S rDNA with different reference species from the genera Bacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Alicyclobacillus, Halobacillus, Virgibacillus, Amphibacillus, Coprobacillus and Gracilibacillus indicated that the isolated strains were highly related to the genus Paenibacillus. Strain B.3T formed an evolutionary lineage distinct from other species within the evolutionary radiation encompassing the genus Paenibacillus. Strain B.3T was a close relative of Paenibacillus polymyxa, but DNA-DNA relatedness data with this species was very low (relative binding ratio < 16%). Based on the morphological and physiological characteristics, as well as on the phylogenetic position determined by 16S rDNA analysis and DNA-DNA relatedness data, it is concluded that these strains should be designated a novel species, for which the name Paenibacillus jamilae sp. nov. is proposed. The type strain is B.3T (= CECT 5266T = DSM 13815T).

Heliophilum fasciatum gen. nov. sp. nov. and Heliobacterium gestii sp. nov.: endospore-forming heliobacteria from rice field soils

Two new taxa of phototrophic heliobacteria are described: Heliobacterium gestii sp. nov. and Heliophilum fasciatum gen. nov. sp. nov. Both organisms were isolated from dry paddy soils. Cells of H. gestii were motile spirilla; cells of H. fasciatum formed cell bundles that were motile as units. Both organisms produced endospores; H. gestii endospores contained dipicolinic acid and elevated levels of calcium. As with other heliobacteria, bacteriochlorophyll g was produced in both organisms and no intracytoplasmic photosynthetic membranes were observed. Growth of H. gestii and H. fasciatum occurred under both photoheterotrophic and chemotrophic conditions; nitrogen fixation also occurred in both organisms. H. gestii and H. fasciatium showed a phylogenetic relationship to the "low GC" line of gram-positive Bacteria, but H. fasciatum was distinct from H. gestii and all other heliobacteria. The ability of H. gestii and H. fasciatum to form endospores might be a significant ecological advantage for survival in their rice soil habitat.