Prebiotic supplements correct oral probiotic deficiency for lasting allergy relief.

The prevalence of allergic rhinitis (common allergies) has increased in the last fifty years, from less than one percent to more than twenty-six percent of the population. Today, more than one hundred million people in the US suffer seasonal or yearlong allergies. The hygiene hypothesis was proposed 30 years ago as a potential explanation for this phenomenon, and we built on it with the specific oral hygiene hypothesis. Our longitudinal pilot study suggested that oral probiotic deficiency is the cause of allergic rhinitis. This clinical trial served to verify our theory and evaluate the effectiveness of AllerPops for allergy relief. We carried out a phase II, randomized, double-blind, controlled, single-center 21-day study to investigate the efficacy of AllerPops to reduce nasal symptoms in 72 adult volunteers with seasonal/year-long nasal allergies and its impact on oral microbiome using amplicon sequencing of 16S ribosome RNA genes. The volunteers were randomly separated into two equally sized groups: a control group and an investigational group. Both groups were given at least three doses of AllerPops, taken every other day, and asked to answer questions about observed allergy symptoms. Volunteers in the investigational group cleaned their mouths before taking a dose and slowly dissolve the lozenge, while those in the control did not. Through this trial, we show that AllerPops prebiotic supplements are effective in providing sustained allergy relief (P = 0.002) and can modulate oral beneficial bacteria that produce short-chain fatty acids (SCFA), such as Fusobacteria, Butyrivibrio, and Peptostreptococcus. The clinical improvements correlated with changes in the relative abundance of probiotics significantly: Fusobacteria (R = 0.32, P = 0.009), Butyrivibrio (R = 0.25, P = 0.044), and Peptostreptococcus (R = 0.34, P = 0.005). These results point to the root cause of allergic rhinitis: the lack of oral probiotics that produce SCFA to pacify the immune systems. Future study of AllerPops' theory will help society redefine the best oral hygiene practice to protect oral probiotics so that we may prevent allergic and autoimmune diseases and dental/gum infections. The trial was retrospectively registered at clinicaltrials.com, with registration number NCT05956691, on 21/07/2023.

High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.

Here, we report the high-quality draft genome sequences of four phylogenetically diverse lignocellulose-degrading bacteria isolated from tropical soil (Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the genetic basis of their ability to degrade lignocellulose. These isolates may provide novel enzymes for biofuel production.

Genome Sequence of Porphyromonas gingivalis Strain A7A1-28.

Porphyromonas gingivalis is an oral opportunistic pathogen. Sequenced P. gingivalis laboratory strains display limited diversity in antigens that modulate host responses. Here, we present the genome sequence of A7A1-28, a strain possessing atypical fimbrillin and capsule types, with a single contig of 2,249,024 bp and a G+C content of 48.58%.

Genome Sequence of Porphyromonas gingivalis Strain 381.

Porphyromonas gingivalis is associated with both oral and systemic diseases. Strain-specific P. gingivalis invasion phenotypes do not reliably predict disease presentation during in vivo studies. Here, we present the genome sequence of 381, a common laboratory strain, with a single contig of 2,378,872 bp and a G+C content of 48.36%.

Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication.

BACKGROUND: Premastication, the transfer of pre-chewed food, is a common infant and young child feeding practice among the Tsimane, forager-horticulturalists living in the Bolivian Amazon. Research conducted primarily with Western populations has shown that infants harbor distinct oral microbiota from their mothers. Premastication, which is less common in these populations, may influence the colonization and maturation of infant oral microbiota, including via transmission of oral pathogens. We collected premasticated food and saliva samples from Tsimane mothers and infants (9-24 months of age) to test for evidence of bacterial transmission in premasticated foods and overlap in maternal and infant salivary microbiota. We extracted bacterial DNA from two premasticated food samples and 12 matched salivary samples from maternal-infant pairs. DNA sequencing was performed with MiSeq (Illumina). We evaluated maternal and infant microbial composition in terms of relative abundance of specific taxa, alpha and beta diversity, and dissimilarity distances. RESULTS: The bacteria in saliva and premasticated food were mapped to 19 phyla and 400 genera and were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The oral microbial communities of Tsimane mothers and infants who frequently share premasticated food were well-separated in a non-metric multi-dimensional scaling ordination (NMDS) plot. Infant microbiotas clustered together, with weighted Unifrac distances significantly differing between mothers and infants. Infant saliva contained more Firmicutes (p < 0.01) and fewer Proteobacteria (p < 0.05) than did maternal saliva. Many genera previously associated with dental and periodontal infections, e.g. Neisseria, Gemella, Rothia, Actinomyces, Fusobacterium, and Leptotrichia, were more abundant in mothers than in infants. CONCLUSIONS: Salivary microbiota of Tsimane infants and young children up to two years of age do not appear closely related to those of their mothers, despite frequent premastication and preliminary evidence that maternal bacteria is transmitted to premasticated foods. Infant physiology and diet may constrain colonization by maternal bacteria, including several oral pathogens.

Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34.

Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

A specific hygiene hypothesis.

Allergic diseases have reached epidemic proportions in Western populations in the last several decades. The hygiene hypothesis proposed more than twenty years ago has helped us to understand the epidemic and has been verified with numerous studies. However, translational measures deduced from these studies to prevent allergic diseases have not proven effective. Recent studies on immigrants' allergies and any potential association between oral infection and allergic diseases prompt me to propose a specific hygiene hypothesis to explain how oral hygiene practices might have contributed to the uprising of hay fever, the most common allergic disease. The historic oral hygiene level in US is closely associated with the emerging allergic epidemic. Future studies to test the hypothesis are needed and verification of the hypothesis can potentially yield highly effective measures to prevent allergic diseases.

Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)).

Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1(T) is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1(T) is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.

Improved lysis of single bacterial cells by a modified alkaline-thermal shock procedure.

Single-cell genomics (SCG) is a recently developed tool to study the genomes of unculturable bacterial species. SCG relies on multiple-strand displacement amplification (MDA), PCR, and next-generation sequencing (NGS); however, obtaining sufficient amounts of high-quality DNA from samples is a major challenge when performing this technique. Here we present an improved bacterial cell lysing procedure that combines incubation in an alkaline buffer with a thermal shock (freezing/heating) treatment to yield highly intact genomic DNA with high efficiency. This procedure is more efficient in lysing Bacillus subtilis and Synechocystis cells compared with two other frequently used lysis methods. Furthermore, 16S ribosomal RNA gene and overall genome recovery were found to be improved by this method using single cells from a Utah desert soil community or Escherichia coli single cells, respectively. The efficiency of genome recovery for E. coli single cells using our procedure is comparable with that of the REPLI-g Single Cell (sc) Kit, but our method is much more economical. By providing high-quality genome templates suitable for downstream applications, our procedure will be a promising improvement for SCG research.

Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos.

Bradyrhizobium sp. WSM1253 is a novel N2-fixing bacterium isolated from a root nodule of the herbaceous annual legume Ornithopus compressus that was growing on the Greek Island of Sifnos. WSM1253 emerged as a strain of interest in an Australian program that was selecting inoculant quality bradyrhizobial strains for inoculation of Mediterranean species of lupins (Lupinus angustifolius, L. princei, L. atlanticus, L. pilosus). In this report we describe, for the first time, the genome sequence information and annotation of this legume microsymbiont. The 8,719,808 bp genome has a G + C content of 63.09 % with 71 contigs arranged into two scaffolds. The assembled genome contains 8,432 protein-coding genes, 66 RNA genes and a single rRNA operon. This improved-high-quality draft rhizobial genome is one of 20 sequenced through a DOE Joint Genome Institute 2010 Community Sequencing Project.

Genome Sequence of Porphyromonas gingivalis Strain AJW4.

Porphyromonas gingivalis is associated with oral and systemic diseases. Strain-specific P. gingivalis invasion phenotypes have been correlated with disease presentation in infected laboratory animals. Here, we present the genome sequence of AJW4, a minimally invasive strain, with a single contig of 2,372,492 bp and a G+C content of 48.27%.

High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym.

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICEMlSym(R7A), also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. The high-quality draft genome is arranged in 70 scaffolds of 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.

Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding phenanthrene degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3' end a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Determination of the complete genome sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH biodegradation that may shape the process in the environment.

Genome Sequence of Porphyromonas gingivalis Strain A7436.

Porphyromonas gingivalis is strongly associated with periodontitis. P. gingivalis strain trafficking and tissue homing differ widely, even among presumptive closely related strains, such as W83 and A7436. Here, we present the genome sequence of A7436 with a single contig of 2,367,029 bp and a G+C content of 48.33%.

Complete Genome Sequence of "Candidatus Liberibacter africanus," a Bacterium Associated with Citrus Huanglongbing.

We report here the complete genome sequence of "Candidatus Liberibacter africanus" strain PTSAPSY. The 1,192,232-bp genome with 34.5% G+C content comprises 1,017 open reading frames, 44 tRNAs, and three complete rRNAs in a circular chromosome.

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species.

Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, and aquaculture settings worldwide. We report here the isolation, characterization, and genome sequence of a novel Vibrio species, Vibrio antiquarius, isolated from a mesophilic bacterial community associated with hydrothermal vents located along the East Pacific Rise, near the southwest coast of Mexico. Genomic and phenotypic analysis revealed V. antiquarius is closely related to pathogenic Vibrio species, namely Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, and Vibrio vulnificus, but sufficiently divergent to warrant a separate species status. The V. antiquarius genome encodes genes and operons with ecological functions relevant to the environment conditions of the deep sea and also harbors factors known to be involved in human disease caused by freshwater, coastal, and brackish water vibrios. The presence of virulence factors in this deep-sea Vibrio species suggests a far more fundamental role of these factors for their bacterial host. Comparative genomics revealed a variety of genomic events that may have provided an important driving force in V. antiquarius evolution, facilitating response to environmental conditions of the deep sea.

Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes.

The Opitutaceae bacterium strain TAV5, a member of the phylum Verrucomicrobia, was isolated from the wood-feeding termite hindgut. We report here its complete genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and 99,831 bp, respectively. The genomic analysis reveals genes for methylotrophy, lignocellulose degradation, and ammonia and sulfate assimilation.

Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets.

We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean wastewater treatment facility using gel microdroplets (GMDs) and single-cell genomics (SCG). This approach provided a single clonal microcolony that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically relevant Thauera species.

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.

Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

Adaptation genomics of a small-colony variant in a Pseudomonas chlororaphis 30-84 biofilm.

The rhizosphere-colonizing bacterium Pseudomonas chlororaphis 30-84 is an effective biological control agent against take-all disease of wheat. In this study, we characterize a small-colony variant (SCV) isolated from a P. chlororaphis 30-84 biofilm. The SCV exhibited pleiotropic phenotypes, including small cell size, slow growth and motility, low levels of phenazine production, and increased biofilm formation and resistance to antimicrobials. To better understand the genetic alterations underlying these phenotypes, RNA and whole-genome sequencing analyses were conducted comparing an SCV to the wild-type strain. Of the genome's 5,971 genes, transcriptomic profiling indicated that 1,098 (18.4%) have undergone substantial reprograming of gene expression in the SCV. Whole-genome sequence analysis revealed multiple alterations in the SCV, including mutations in yfiR (cyclic-di-GMP production), fusA (elongation factor), and cyoE (heme synthesis) and a 70-kb deletion. Genetic analysis revealed that the yfiR locus plays a major role in controlling SCV phenotypes, including colony size, growth, motility, and biofilm formation. Moreover, a point mutation in the fusA gene contributed to kanamycin resistance. Interestingly, the SCV can partially switch back to wild-type morphologies under specific conditions. Our data also support the idea that phenotypic switching in P. chlororaphis is not due to simple genetic reversions but may involve multiple secondary mutations. The emergence of these highly adherent and antibiotic-resistant SCVs within the biofilm might play key roles in P. chlororaphis natural persistence.