Halomonas, a newly recognized human pathogen causing infections and contamination in a dialysis center: three new species

Identification and analysis of a clinically isolated strain of Halomonas based on whole-genome sequencing and comparative genomics

OBJECTIVE

The aim of this study was to identify the species of a Halomonas strain isolated from a neonatal blood sample and to understand the potential pathogenicity and characteristic genes of the strain.

METHODS

The genomic DNA of strain 18071143 (identified as Halomonas by matrix-assisted laser desorption-ionization time of flight-mass spectrometry and the 16S ribosomal RNA (rRNA) gene sequence) was sequenced using Nanopore PromethION platforms. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were calculated using the complete genome sequences of the strain. Comparative genomic analyses were performed on strain 18071143 and 3 strains of Halomonas (Halomonas stevensii S18214, Halomonas hamiltonii KCTC 22154, and Halomonas johnsoniae KCTC 22157) that were associated with human infections and had high genomic similarity to strain 18071143.

RESULTS

Phylogenetic, ANI, and dDDH similarity analyses based on genome sequence indicated that strain 18071143 belonged to the species H stevensii. Similarities exist between strain 18071143 and the other 3 Halomonas strains in terms of gene structure and protein function. Nonetheless, strain 18071143 has greater potential for DNA replication, recombination, repair, and horizontal transfer.

CONCLUSION

Whole-genome sequencing holds great promise for accurate strain identification in clinical microbiology. In addition, the results of this study provide data for understanding Halomonas from the perspective of pathogenic bacteria.

Development of Martian saline seep models and their implications for planetary protection

While life on Mars has not been found, Earth-based microorganisms may contaminate the Red Planet during rover expeditions and human exploration. Due to the survival advantages conferred by the biofilm morphology to microorganisms, such as resistance to UV and osmotic stress, biofilms are particularly concerning from a planetary protection perspective. Modeling and data from the NASA Phoenix mission indicate that temporary liquid water might exist on Mars in the form of high salinity brines. These brines could provide colonization opportunities for terrestrial microorganisms brought by spacecraft or humans. To begin testing for potential establishment of microbes, results are presented from a simplified laboratory model of a Martian saline seep inoculated with sediment from Hailstone Basin, a terrestrial saline seep in Montana (USA). The seep was modeled as a sand-packed drip flow reactor at room temperature fed media with either 1 M MgSO₄ or 1 M NaCl. Biofilms were established within the first sampling point of each experiment. Endpoint 16S rRNA gene community analysis showed significant selection of halophilic microorganisms by the media. Additionally, we detected 16S rRNA gene sequences highly similar to microorganisms previously detected in two spacecraft assembly cleanrooms. These experimental models provide an important foundation for identifying microbes that could hitch-hike on spacecraft and may be able to colonize Martian saline seeps. Future model optimization will be vital to informing cleanroom sterilization procedures.

Comparative analysis of the gut bacteria of the relict gull (Larus Relictus) and black-necked grebe (Podiceps Nigricollis) in Erdos Relic Gull National Nature Reserve in Inner Mongolia, China

The gut microbiota promotes host health by maintaining homeostasis and enhancing digestive efficiency. The gut microflora in wild birds affects host physiological characteristics, nutritional status, and stress response. The relict gull (Larus Relictus, a Chinese national first-class protected species) and the black-necked grebe (Podiceps Nigricollis, a secondary protected species) bred in the Ordos Relic Gull National Nature Reserve share similar feeding habits and living environments but are distantly related genetically. To explore the composition and differences in the gut microbiota of these two key protected avian species in Erdos Relic Gull National Nature Reserve and provide a basis for their protection, 16S rRNA gene high-throughput sequencing was performed and the gut microbial diversity and composition of the relict gull (L. Relictus) and black-necked grebe (P. Nigricollis) was characterized. In total, 445 OTUs (operational taxonomic units) were identified and classified into 15 phyla, 22 classes, 64 orders, 126 families, and 249 genera. Alpha diversity analysis indicates that the gut microbial richness of the relict gull is significantly lower than that of the black-necked grebe. Gut microbe composition differs significantly between the two species. The most abundant bacterial phyla in these samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes. The prominent phylum in the relict gull was Proteobacteria, whereas the prominent phylum in the black-necked grebe was Firmicutes. The average relative abundance of the 17 genera identified was greater than 1%. The dominant genus in the relict gull was Escherichia-Shigella, whereas Halomonas was dominant in the black-necked grebe. Microbial functional analyses indicate that environmental factors exert a greater impact on relict gulls than on black-necked grebes. Compared with the relict gull, the black-necked grebe was able to use food more efficiently to accumulate its nutrient requirements, and the gut of the relict gull harbored more pathogenic bacteria, which may be one reason for the decline in the relict gull population, rendering it an endangered species. This analysis of the gut microbial composition of these two wild avian species in the same breeding grounds is of great significance, offers important guidance for the protection of these two birds, especially relict gulls, and provides a basis for understanding the propagation of related diseases.

Otitis Media in Children with Down Syndrome Is Associated with Shifts in the Nasopharyngeal and Middle Ear Microbiotas

Background: Otitis media (OM) is defined as middle ear (ME) inflammation that is usually due to infection. Globally, OM is a leading cause of hearing loss and is the most frequently diagnosed disease in young children. For OM, pediatric patients with Down syndrome (DS) demonstrate higher incidence rates, greater severity, and poorer outcomes. However, to date, no studies have investigated the bacterial profiles of children with DS and OM. Method: We aimed to determine if there are differences in composition of bacterial profiles or the relative abundance of individual taxa within the ME and nasopharyngeal (NP) microbiotas of pediatric OM patients with DS (n = 11) compared with those without DS (n = 84). We sequenced the 16S rRNA genes and analyzed the sequence data for diversity indices and relative abundance of individual taxa. Results: Individuals with DS demonstrated increased biodiversity in their ME and NP microbiotas. In children with OM, DS was associated with increased biodiversity and higher relative abundance of specific taxa in the ME. Conclusion: Our findings suggest that dysbioses in the NP of DS children contributes to their increased susceptibility to OM compared with controls. These findings suggest that DS influences regulation of the mucosal microbiota and contributes to OM pathology.

East Asian monsoon manipulates the richness and taxonomic composition of airborne bacteria over China coastal area

Airborne bacteria may have significant impacts on aerosol properties, public health and ecosystem depending on their taxonomic composition and transport. This study investigated the seasonal and spatial variations of bacterial composition and richness over the east coast of China and the roles of East Asian monsoon played through synchronous sampling and 16S rRNA sequencing analysis of airborne bacteria at Huaniao island of the East China Sea (ECS) and the urban and rural sites of Shanghai. Airborne bacteria showed higher richness over the land sites than Huaniao island with the highest values found in the urban and rural springs associated with the growing plants. For the island, the maximal richness occurred in winter as the result of prevailing terrestrial winds controlled by East Asian winter monsoon. Proteobacteria, Actinobacteria and Cyanobacteria were found to be top three phyla, together accounting for 75 % of total airborne bacteria. Radiation-resistant Deinococcus, Methylobacterium belonging to Rhizobiales (related to vegetation) and Mastigocladopsis_PCC_10914 originating from marine ecosystem were indicator genera for urban, rural and island sites, respectively. The Bray-Curits dissimilarity of taxonomic composition between the island and two land sites was the lowest in winter with the representative genera over island also typically from the soil. Our results reveal that seasonal change of monsoon wind directions evidently affects the richness and taxonomic composition of airborne bacteria in China coastal area. Particularly, prevailing terrestrial winds lead to the dominance of land-derived bacteria over the coastal ECS which may have a potential impact on marine ecosystem.

Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection

BACKGROUND

The human microbiome plays an important role in modulating the host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral pharynx in the context of SARS-CoV-2 and other viral infections; hence, to broaden our understanding of host-viral responses in general and to deepen our knowledge of COVID-19, we performed a large-scale, systematic evaluation of the effect of SARS-CoV-2 infection on human microbiota in patients with varying disease severity.

RESULTS

We processed 521 samples from 203 COVID-19 patients with varying disease severity and 94 samples from 31 healthy donors, consisting of 213 pharyngeal swabs, 250 sputa, and 152 fecal samples, and obtained meta-transcriptomes as well as SARS-CoV-2 sequences from each sample. Detailed assessment of these samples revealed altered microbial composition and function in the upper respiratory tract (URT) and gut of COVID-19 patients, and these changes are significantly associated with disease severity. Moreover, URT and gut microbiota show different patterns of alteration, where gut microbiome seems to be more variable and in direct correlation with viral load; and microbial community in the upper respiratory tract renders a high risk of antibiotic resistance. Longitudinally, the microbial composition remains relatively stable during the study period.

CONCLUSIONS

Our study has revealed different trends and the relative sensitivity of microbiome in different body sites to SARS-CoV-2 infection. Furthermore, while the use of antibiotics is often essential for the prevention and treatment of secondary infections, our results indicate a need to evaluate potential antibiotic resistance in the management of COVID-19 patients in the ongoing pandemic. Moreover, a longitudinal follow-up to monitor the restoration of the microbiome could enhance our understanding of the long-term effects of COVID-19. Video Abstract.

Heat stress in pigs and broilers: role of gut dysbiosis in the impairment of the gut-liver axis and restoration of these effects by probiotics, prebiotics and synbiotics

Heat stress is one of the most challenging stressors for animal production due to high economic losses resulting from impaired animal’s productivity, health and welfare. Despite the fact that all farm animal species are susceptible to heat stress, birds and pigs are particularly sensitive to heat stress due to either lacking or non-functional sweat glands. Convincing evidence in the literature exists that gut dysbiosis, a term used to describe a perturbation of commensal gut microbiota, develops in broilers and pigs under heat stress. Owing to the protective role of commensal bacteria for the gut barrier, gut dysbiosis causes a disruption of the gut barrier leading to endotoxemia, which contributes to the typical characteristics of heat stressed broilers and growing and growing-finishing pigs, such as reduced feed intake, decreased growth and reduced lean carcass weight. A substantial number of studies have shown that feeding of probiotics, prebiotics and synbiotics is an efficacious strategy to protect broilers from heat stress-induced gut barrier disruption through altering the gut microbiota and promoting all decisive structural, biochemical, and immunological elements of the intestinal barrier. In most of the available studies in heat stressed broilers, the alterations of gut microbiota and improvements of gut barrier function induced by feeding of either probiotics, prebiotics or synbiotics were accompanied by an improved productivity, health and/or welfare when compared to non-supplemented broilers exposed to heat stress. These findings indicate that the restoration of gut homeostasis and function is a key target for dietary interventions aiming to provide at least partial protection of broilers from the detrimental impact of heat stress conditions. Despite the fact that the number of studies dealing with the same feeding strategy in heat stressed pigs is limited, the available few studies suggest that feeding of probiotics might also be a suitable approach to enhance productivity, health and welfare in pigs kept under heat stress conditions. 

Purulent lymphadenitis due to Halomonas hamiltonii: a case report

Halomonas hamiltonii is a gram-negative rod bacterium isolated from highly saline environments. H. hamiltonii has rarely been reported as a human pathogen. Herein, we present the first case report of a purulent lymphadenitis caused by H. hamiltonii worldwide. The patient was a previously healthy girl aged 1 year who was referred to our hospital for left axillary lymphadenitis. Although oral amoxicillin was administered, lymphadenitis did not improve, and an abscess developed. After incision and drainage, the abscess was reduced. No recurrence of lymphadenitis was observed. The pus culture was negative. However, the 16S ribosomal DNA was amplified by the melting temperature mapping method. The amplified 16S ribosomal DNA sequence revealed 99.7% identity of H. hamiltonii. To the best of our knowledge, this is the first case of H. hamiltonii infection in a lymph node. This pathogen should be considered when diagnosing purulent lymphadenitis in healthy patients with lymphadenopathy of unknown origin.

Pollution Indicators and HAB-Associated Halophilic Bacteria Alongside Harmful Cyanobacteria in the Largest Mussel Cultivation Area in Greece

Taking into consideration the essential contribution of Mytilus galloprovincialis farming, it is of rising importance to add knowledge regarding bacterial species occurrence in water samples from aquaculture zones from the point of view of both the organism and public health. In the present study, we investigated the bacterial community existing in water samples from six Mytilus galloprovincialis aquaculture areas in the Thermaikos gulf, northern Greece, that may provoke toxicity in aquatic organisms and humans and may indicate environmental pollution in mussel production as well as algal blooms. Bacterial species were identified molecularly by sequencing of a partial 16s rRNA segment and were analyzed phylogenetically for the confirmation of the bacterial taxonomy. The results obtained revealed the presence of four bacterial genera (Halomonas sp., Planococcus sp., Sulfitobacter sp., and Synechocystis sp.). Members of the Halomonas and Sulfitobacter genera have been isolated from highly polluted sites, Planococcus bacteria have been identified in samples derived directly from plastic debris, and Synechocystis bacteria are in line with microcystin detection. In this context, the monitoring of the bacteria community in mussel aquaculture water samples from the Thermaikos gulf, the largest mussel cultivation area in Greece, represents an indicator of water pollution, microplastics presence, algal blooms, and toxin presence.

Molting Alters the Microbiome, Immune Response, and Digestive Enzyme Activity in Mud Crab (Scylla paramamosain)

Molting is a crucial lifelong process in the growth, development, and reproduction of crustaceans. In mud crab (Scylla paramamosain), new exoskeleton, gills, and appendages are formed after a molting, which contributes to a 40 to 90% increase in body weight. However, little is currently known about the associations between molting and the dynamic changes of microbiota and physiological characteristics in mud crabs. In this study, the effects of molting on changes of the microbiome, immune response, and digestive enzyme activities in mud crabs were investigated. The results showed dynamic changes in the abundances and community compositions of crab-associated microbiota harboring the gills, subcuticular epidermis, hepatopancreas, midgut, and hemolymph during molting. Renewed microbiota was observed in the gills and midgut of crabs at the postmolt stages, which seems to be related to the formation of a new exoskeleton after the molting. A significant positive correlation between the expression of two antimicrobial peptide (AMP) genes (SpALF5 and SpCrustin) and the relative abundance of two predominant microorganisms (Halomonas and Shewanella) in hemolymph was observed in the whole molt cycle, suggesting that AMPs play a role in modulating hemolymph microbiota. Furthermore, digestive enzymes might play a vital role in the changes of microbiota harboring the hepatopancreas and midgut, which provide suitable conditions for restoring and reconstructing host-microbiome homeostasis during molting. In conclusion, this study confirms that molting affects host-associated microbiota and further sheds light on the effects on the immune response and the digestive systems as well. IMPORTANCE Molting is crucial for crustaceans. In mud crab, its exoskeleton is renewed periodically during molting, and this process is an ideal model to study the effects of host development on its microbiota. Here, multiple approaches were used to investigate the changes in microbial taxa, immune response, and digestive enzyme activity with respect to molting in mud crab. The results found that a renewed microbiota was generated in the gills and midgut of crab after a molt. A significant positive correlation between changes in the relative abundances of microbes (such as Halomonas and Shewanella) and the expression of AMP genes (SpALF5 and SpCrustin) was observed in the hemolymph of crabs during the whole molt cycle, suggesting the modulation of hemolymph microbes by AMPs. Furthermore, the digestive enzymes were found to participate in the regulation of microbiota in hepatopancreas and midgut, consequently providing a suitable condition for the restoration and reconstruction of host-microbiome homeostasis during the molting. This study confirms that molting affects the microbial communities and concomitantly influences the immune and digestive systems in mud crabs. This is also the first time the homeostasis of the host and microbiome, and the associations between molting and physiological characteristics in crustaceans, have been revealed.

A Metatranscriptomics Survey of Microbial Diversity on Surfaces Post-Intervention of cleanSURFACES® Technology in an Intensive Care Unit

Hospital-acquired infections (HAIs) pose a serious threat to patients, and hospitals spend billions of dollars each year to reduce and treat these infections. Many HAIs are due to contamination from workers’ hands and contact with high-touch surfaces. Therefore, we set out to test the efficacy of a new preventative technology, AIONX^® Antimicrobial Technologies, Inc’s cleanSURFACES^®, which is designed to complement daily chemical cleaning events by continuously preventing re-colonization of surfaces. To that end, we swabbed surfaces before (Baseline) and after (Post) application of the cleanSURFACES^® at various time points (Day 1, Day 7, Day 14, and Day 28). To circumvent limitations associated with culture-based and 16S rRNA gene amplicon sequencing methodologies, these surface swabs were processed using metatranscriptomic (RNA) analysis to allow for comprehensive taxonomic resolution and the detection of active microorganisms. Overall, there was a significant (P < 0.05) global reduction of microbial diversity in Post-intervention samples. Additionally, Post sample microbial communities clustered together much more closely than Baseline samples based on pairwise distances calculated with the weighted Jaccard distance metric, suggesting a defined shift after product application. This shift was characterized by a general depletion of several microbes among Post samples, with multiple phyla also being reduced over the duration of the study. Notably, specific clinically relevant microbes, including Staphylococcus aureus, Clostridioides difficile and Streptococcus spp., were depleted Post-intervention. Taken together, these findings suggest that chemical cleaning events used jointly with cleanSURFACES^® have the potential to reduce colonization of surfaces by a wide variety of microbes, including many clinically relevant pathogens.

Chronic Intermittent Hypoxia Participates in the Pathogenesis of Atherosclerosis and Perturbs the Formation of Intestinal Microbiota

Chronic intermittent hypoxia (CIH) is the prominent signature of highly prevalent obstructive sleep apnea (OSA) pathophysiology, which leads to increased risk and aggravation of atherosclerotic cardiovascular diseases. However, whether intestinal microbiota is implicated in the mechanisms linking CIH to arteriosclerosis (AS) pathogenesis remains unclear. The association of CIH with the development of altered gut microbiota (GM) may provide the opportunity to develop preventive strategies for atherosclerotic cardiovascular risk reduction. Animal models of apolipoprotein E-deficient (apoE^-/-) mice treated with high-fat diet (HFD) and subjected to CIH conditions was applied to mimic the AS observed in patients with OSA. The physiological status and atherosclerotic lesion formation were confirmed by histological analysis. 16S rDNA sequencing of fecal samples was conducted to determine the changes in gut microbial composition. Morphometric analysis demonstrated that CIH caused aggravated atherosclerotic lesions and facilitated AS in apoE^-/- mice treated with HFD. The gut bacteria was significantly varied in AS and AS+CIH mice compared with that in the control mice. Significantly perturbed GM profiles were detected in AS mice with and without CIH, with altered microbial α- and β- diversity and shifts in bacterial compositions at phylum and genus levels. While the difference between AS and AS+CIH was observed at different bacteria taxa levels. Aggravation of reduced Sutterella and increased Halomonas, Halomonadaceae and Oceanospirillales was noted in CIH-treated AS mice. The correlation of intestinal bacterial parameters with pathological changes in artery indicated complicated interactions under CIH-induced GM dysbiosis. Furthermore, the gut microbial functions in the potential ability of replication recombination and repair proteins, glycan biosynthesis and metabolism, as well as metabolism of cofactors and vitamins were identified to be further suppressed by CIH. Our findings demonstrated a causal effect of CIH on GM alterations in AS mice and suggested that the disordered GM features in AS development were deteriorated by CIH, which may be associated with AS aggravation. Preventative strategies targeting gut microbiome are highly recommended for intervention of OSA-related AS.

Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage

The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.

NaCl Concentration-Dependent Aminoglycoside Resistance of Halomonas socia CKY01 and Identification of Related Genes

Among various species of marine bacteria, those belonging to the genus Halomonas have several promising applications and have been studied well. However, not much information has been available on their antibiotic resistance. In our efforts to learn about the antibiotic resistance of strain Halomonas socia CKY01, which showed production of various hydrolases and growth promotion by osmolytes in previous study, we found that it exhibited resistance to multiple antibiotics including kanamycin, ampicillin, oxacillin, carbenicillin, gentamicin, apramycin, tetracycline, and spectinomycin. However, the H. socia CKY01 resistance pattern to kanamycin, gentamicin, apramycin, tetracycline, and spectinomycin differed in the presence of 10% NaCl and 1% NaCl in the culture medium. To determine the mechanism underlying this NaCl concentration-dependent antibiotic resistance, we compared four aminoglycoside resistance genes under different salt conditions while also performing time-dependent reverse transcription PCR. We found that the aph2 gene encoding aminoglycoside phosphotransferase showed increased expression under the 10% rather than 1% NaCl conditions. When these genes were overexpressed in an Escherichia coli strain, pETDuet-1::aph2 showed a smaller inhibition zone in the presence of kanamycin, gentamicin, and apramycin than the respective control, suggesting aph2 was involved in aminoglycoside resistance. Our results demonstrated a more direct link between NaCl and aminoglycoside resistance exhibited by the H. socia CKY01 strain.

16s rRNA metagenomic analysis reveals predominance of Crtl and CruF genes in Arabian Sea coast of India

Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.

Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model

BACKGROUND

Undernutrition is a prevalent and spontaneous condition in animal production which always affects microbiota-host interaction in gastrointestinal tract. However, how undernutrition affects crosstalk homeostasis is largely unknown. Here, we discover how undernutrition affects microbial profiles and subsequently how microbial metabolism affects the signal transduction and tissue renewal in ruminal epithelium, clarifying the detrimental effect of undernutrition on ruminal homeostasis in a pregnant sheep model.

RESULTS

Sixteen pregnant ewes (115 days of gestation) were randomly and equally assigned to the control (CON) and severe feed restriction (SFR) groups. Ewes on SFR treatment were restricted to a 30% level of ad libitum feed intake while the controls were fed normally. After 15 days, all ewes were slaughtered to collect ruminal digesta for 16S rRNA gene and metagenomic sequencing and ruminal epithelium for transcriptome sequencing. Results showed that SFR diminished the levels of ruminal volatile fatty acids and microbial proteins and repressed the length, width, and surface area of ruminal papillae. The 16S rRNA gene analysis indicated that SFR altered the relative abundance of ruminal bacterial community, showing decreased bacteria about saccharide degradation (Saccharofermentans and Ruminococcus) and propionate genesis (Succiniclasticum) but increased butyrate producers (Pseudobutyrivibrio and Papillibacter). Metagenome analysis displayed that genes related to amino acid metabolism, acetate genesis, and succinate-pathway propionate production were downregulated upon SFR, while genes involved in butyrate and methane genesis and acrylate-pathway propionate production were upregulated. Transcriptome and real-time PCR analysis of ruminal epithelium showed that downregulated collagen synthesis upon SFR lowered extracellular matrix-receptor interaction, inactivated JAK3-STAT2 signaling pathway, and inhibited DNA replication and cell cycle.

CONCLUSIONS

Generally, undernutrition altered rumen bacterial community and function profile to decrease ruminal energy retention, promoted epithelial glucose and fatty acid catabolism to elevate energy supply, and inhibited the proliferation of ruminal epithelial cells. These findings provide the first insight into the systemic microbiota-host interactions that are involved in disrupting the ruminal homeostasis under a malnutrition pattern. Video Abstract.

An Assessment of the Bacterial Diversity found in Dental Unit Waterlines using the Illumina MiSeq

Water from the waterlines of dental units is often contaminated with bacteria but there have been few studies accurately assessing the diversity of these bacterial populations. The aim of our study was to assess the bacterial diversity present in water collected from dental unit waterlines using the Illumina MiSeq. Water was collected from two separate dental units located in a dental hospital and two units found in two separate private clinics in Gangneung-si, Korea. From the four water samples that were analyzed, a total of 233 bacterial genera were identified. The most abundant genera were Sphingomonas (25%), Halomonas (20%), Reyranella (8%), and Novosphingobium (6%). Halomonas was more prevalent in the two dental units located at the dental hospital, while Reyranella and Sphingomonas were more commonly found in the private dental clinics. Only 19 of the 233 identified genera were common between water samples from all dental units. Opportunistic pathogens were shown to account for 7.7% of the total bacterial genera identified. Our results have demonstrated that there is a wide assortment of bacterial genera present in dental unit waterlines.

Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings

Aquatic ecosystems harbor a vast pool of antibiotic resistance genes (ARGs), which can suffer mutation, recombination and selection events. Here, we explored the diversity of ARGs, virulence factors and the bacterial community composition in water samples before (surface raw water, RW) and after (disinfected water, DW) drinking water conventional treatment, as well as in tap water (TW) and ultrafiltration membranes (UM, recovered from hemodialysis equipment) through metagenomics. A total of 852 different ARGs were identified, 21.8% of them only in RW, which might reflect the impact of human activities on the river at the sampling point. Although a similar resistance profile has been observed between the samples, significant differences in the frequency of clinically relevant antibiotic classes (penam and peptide) were identified. Resistance determinants to last resort antibiotics, including sequences related to mcr, optrA and poxtA and clinically relevant beta-lactamase genes (i.e. bla_KPC, bla_GES, bla_IMP, bla_VIM, bla_SPM and bla_NDM) were detected. 830 coding sequences (CDSs - related to 217 different ARGs) were embedded in contigs associated with mobile genetic elements, specially plasmids, of which 68% in RW, DW and TW, suggesting the importance of water environments in resistance dissemination. Shifts in bacterial pathogens genera were observed, such as a significant increase in Mycobacterium after treatment and distribution. In UM, the potentially pathogenic genus Halomonas predominated. Its draft genome was closely related to H. stevensii, hosting mainly multidrug efflux pumps. These results broaden our understanding of the global ARGs diversity and stress the importance of tracking the ever-expanding environmental resistome.

Adsorbed Sulfamethoxazole Exacerbates the Effects of Polystyrene (∼2 μm) on Gut Microbiota and the Antibiotic Resistome of a Soil Collembolan

Microplastics pollution in the environment is now receiving worldwide attention; however, the effects of copollution of antibiotics and microplastics on the gut microbiome of globally distributed and functionally important nontarget soil animals remain poorly understood. We studied a model collembolan (Folsomia candida) and found that the ingestion of microplastics (polystyrene, 2-2.9 μm) substantially altered the gut microbiome, antibiotic resistance gene (ARG) profile, and the isotopic fractionation in the soil collembolan tissue. Importantly, collembolans exposed to polystyrene microplastics loaded with sulfamethoxazole (MA) presented a distinctive gut microbiome, ARG profile, and isotopic fractionation compared to those exposed to polystyrene alone (MH). We observed that the abundance of ARGs and mobile genetic elements (MGEs) in the MA-treated collembolan guts was significantly higher than in the MH and the control treatments. There were also strong interactions between the gut microbiome and ARGs in the collembolan guts. We further found that bacterial β-diversity correlated significantly with the δ¹³C and δ¹⁵N values in collembolan body tissues. Together, our results indicate that changes in isotopic fractionation and ARG profiles in the collembolan were induced by the changes in gut microbiota and suggest that microplastics from diverse sources may have profound influences on soil fauna and soil food webs.

Heat stress affects fecal microbial and metabolic alterations of primiparous sows during late gestation

Background

Heat stress (HS) jeopardizes intestinal barrier functions and augments intestinal permeability in pigs. However, whether HS-induced maternal microbial and metabolic changes in primiparous sows during late gestation remains elusive. We present here, a study investigating the fecal microbial and metabolic responses in late gestational primiparous sows when exposed to HS.

Methods

Twelve first-parity Landrace × Large White F1 sows were randomly assigned into two environmental treatments including the thermoneutral (TN) (18–22 °C; n = 6) and HS (28–32 °C; n = 6) conditions. Both treatments were applied from 85 d of gestation to farrowing. The serum and feces samples were collected on d 107 of gestation, for analyses including intestinal integrity biomarkers, high-throughput sequencing metagenomics, short-chain fatty acid (SCFA) profiles and nontargeted metabolomics.

Results

Our results show that HS group has higher serum Heat shock protein 70 (HSP70), lipopolysaccharide (LPS) and lipopolysaccharide-binding protein (LBP) levels. The gut microbial community can be altered upon HS by using β-diversity and taxon-based analysis. In particular, the relative abundance of genera and operational taxonomic units (OTUs) related to Clostridiales and Halomonas are higher in HS group, the relative abundance of genera and OTUs related to Bacteroidales and Streptococcus, however, are lower in HS group. Results of metabolic analysis reveal that HS lowers the concentrations of propionate, butyrate, total SCFA, succinate, fumarate, malate, lactate, aspartate, ethanolamine, β-alanine and niacin, whereas that of fructose and azelaic acid are higher in HS group. These metabolites mainly affect propanoate metabolism, alanine, aspartate and glutamate metabolism, phenylalanine metabolism, β-alanine metabolism, pantothenate and CoA biosynthesis, tricarboxylic acid cycle (TCA) and nicotinate and nicotinamide metabolism. Additionally, correlation analysis between significant microbes and metabolites indicated that the HS-induced microbiota shift is likely the cause of changes of intestinal metabolism.

Conclusions

Taken together, we reveal characteristic structural and metabolic changes in maternal gut microbiota as a result of late gestational HS, which could potentially provide the basis for further study on offspring gut microbiota and immune programming.

Metagenomic analysis of the effects of toll-like receptors on bacterial infection in the peritoneal cavity following cecum ligation and puncture in mice

Objective

To establish the composition of bacteria in mice following cecum ligation and puncture (CLP) through metagenomic analysis and investigate the role of TLRs on the composition of bacteria.

Methods

Total DNA extraction was done from the ascites, blood, and fecal samples from C57BL/6 mice sacrificed at 0, 4, 8, and 16 h, as well as from Tlr2^–/–, Tlr4^–/–, Tlr5^–/–, and NF-κB^–/–mice sacrificed at 16 h following CLP. Amplification of the V3–V4 regions of the bacterial 16S rRNA genes by PCR and the Illumina MiSeq sequencer was used for deep sequencing. Hierarchical clustering of the isolates was performed with Ward’s method using Euclidean distances. The relative abundance according to operational taxonomic unit (OTU) number or taxa was used to compare the richness among subgroups in the experiments.

Results

There were 18 taxa that had significantly different abundances among the different samples of the C57BL/6 mice at 16 h following CLP. Various dynamic changes in the infectious bacteria inside the peritoneal cavity after CLP were found. While knockout of Tlr5 and NF-κB impaired the ability of bacterial clearance inside the peritoneal cavity for some kinds of bacteria found in the C57BL/6 mice, the knockout of Tlr4 enhanced clearance for other kinds of bacteria, and they presented excessive abundance in the peritoneal cavity despite their scarce abundance in the stool.

Conclusion

NF-κB and TLRs are involved in bacterial clearance and in the expression pattern of the bacterial abundance inside the peritoneal cavity during polymicrobial infection.

Vitamin D and Phenylbutyrate Supplementation Does Not Modulate Gut Derived Immune Activation in HIV-1

Dysbiosis and a dysregulated gut immune barrier function contributes to chronic immune activation in HIV-1 infection. We investigated if nutritional supplementation with vitamin D and phenylbutyrate could improve gut-derived inflammation, selected microbial metabolites, and composition of the gut microbiota. Treatment-naïve HIV-1-infected individuals (n = 167) were included from a double-blind, randomized, and placebo-controlled trial of daily 5000 IU vitamin D and 500 mg phenylbutyrate for 16 weeks (Clinicaltrials.gov NCT01702974). Baseline and per-protocol plasma samples at week 16 were analysed for soluble CD14, the antimicrobial peptide LL-37, kynurenine/tryptophan-ratio, TMAO, choline, and betaine. Assessment of the gut microbiota involved 16S rRNA gene sequencing of colonic biopsies. Vitamin D + phenylbutyrate treatment significantly increased 25-hydroxyvitamin D levels (p < 0.001) but had no effects on sCD14, the kynurenine/tryptophan-ratio, TMAO, or choline levels. Subgroup-analyses of vitamin D insufficient subjects demonstrated a significant increase of LL-37 in the treatment group (p = 0.02), whereas treatment failed to significantly impact LL-37-levels in multiple regression analysis. Further, no effects on the microbiota was found in number of operational taxonomic units (p = 0.71), Shannon microbial diversity index (p = 0.82), or in principal component analyses (p = 0.83). Nutritional supplementation with vitamin D + phenylbutyrate did not modulate gut-derived inflammatory markers or microbial composition in treatment-naïve HIV-1 individuals with active viral replication.

AhlX, an N-acylhomoserine Lactonase with Unique Properties

N-Acylhomoserine lactonase degrades the lactone ring of N-acylhomoserine lactones (AHLs) and has been widely suggested as a promising candidate for use in bacterial disease control. While a number of AHL lactonases have been characterized, none of them has been developed as a commercially available enzymatic product for in vitro AHL quenching due to their low stability. In this study, a highly stable AHL lactonase (AhlX) was identified and isolated from the marine bacterium Salinicola salaria MCCC1A01339. AhlX is encoded by a 768-bp gene and has a predicted molecular mass of 29 kDa. The enzyme retained approximately 97% activity after incubating at 25 °C for 12 days and ~100% activity after incubating at 60 °C for 2 h. Furthermore, AhlX exhibited a high salt tolerance, retaining approximately 60% of its activity observed in the presence of 25% NaCl. In addition, an AhlX powder made by an industrial spray-drying process attenuated Erwinia carotovora infection. These results suggest that AhlX has great potential for use as an in vitro preventive and therapeutic agent for bacterial diseases.

Metagenomic analysis of tarball-associated bacteria from Goa, India

The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.

Effects of tetrakis (hydroxymethyl) phosphonium sulfate pretreatment on characteristics of sewage sludge

Recently, tetrakis(hydroxymethyl)phosphonium sulfate (THPS) was found to play an important role in the sludge pretreatment process. However, the effects of THPS pretreatment on the characteristics of sewage sludge are still insufficiently understood. The properties of sludge after pretreatment with different concentrations of THPS were investigated in this study. The results showed that pH, dewatering ability, and particle size of sludge decreased with increase in THPS concentration. The volatile suspended solids (VSS) and total suspended solids (TSS) of sludge also decreased slightly with increase in THPS concentration. The specific oxygen uptake rate (SOUR) results suggested that lower THPS concentrations (≤1.87 mg/g VSS) enhanced the activity of sludge, but higher concentrations (≥1.87 mg/g VSS) inhibited it. Gram-negative bacteria with peritrichous flagellation (such as Pseudomonas, Escherichia, and Faecalibacterium) were extremely sensitive to THPS. The decrease in specific most probable numbers (MPNs) of pathogens (total coliforms and Escherichia coli) with the increase in THPS concentration also proved the sterilization ability of THPS in the sludge pretreatment process. Pretreatment of sludge with concentrations of THPS higher than 37.41 mg/g VSS would meet the pathogen requirements for land application of Class A biosolids.

Composition and functional diversity of microbial community across a mangrove-inhabited mudflat as revealed by 16S rDNA gene sequences

The gradient distribution of microbial communities has been detected in profiles along many natural environments. In a mangrove seedlings inhabited mudflat, the microbes drive a variety of biogeochemical processes and are associated with a dramatically changed environment across the tidal zones of mudflat. A better understanding of microbial composition, diversity and associated functional profiles in relation to physicochemical influences could provide more insights into the ecological functions of microbes in a coastal mangrove ecosystem. In this study, the variation of microbial community along successive tidal flats inhabited by mangrove seedlings were characterized based on the 16S rDNA gene sequences, and then the factors that shape the bacterial and archaeal communities were determined. Results showed that the tidal cycles strongly influence the distribution of bacterial and archaeal communities. Dissimilarity and gradient distribution of microbial communities were found among high tidal flat, mid-low tidal flat and seawater. Discrepancies were also as well observed from the surface to subsurface layers specifically in the high tidal flat. For example, Alphaproteobacteria displayed an increasing trend from low tidal to high tidal flat and vice versa for Deltaproteobacteria; Cyanobacteria and Thaumarchaeota were more dominant in the surface layer than the subsurface. In addition, by classifying the microorganisms into metabolic functional groups, we were able to identify the biogeochemical pathway that was dominant in each zone. The (oxygenic) photoautotrophy and nitrate reduction were enhanced in the mangrove inhabited mid tidal flat. It revealed the ability of xenobiotic metabolism microbes to degrade, transform, or accumulate environmental hydrocarbon pollutants in seawater, increasing sulfur-related respiration from high tidal to low tidal flat. An opposite distribution was found for major nitrogen cycling processes. The shift of both composition and function of microbial communities were significantly related to light, oxygen availability and total dissolved nitrogen instead of sediment types or salinity.

Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes

INTRODUCTION

The cutaneous microbiome maintains skin barrier function, regulates inflammation, and stimulates wound-healing responses. Burn injury promotes an excessive activation of the cutaneous and systemic immune response directed against commensal and invading pathogens. Skin grafting is the primary method of reconstructing full-thickness burns, and wound infection continues to be a significant complication.

METHODS

In this study, the cutaneous bacterial microbiome was evaluated and subsequently compared to patient outcomes. Three different full-thickness skin specimens were assessed: control skin from non-burned subjects; burn margin from burn patients; and autologous donor skin from the same cohort of burn patients.

RESULTS

We observed that skin bacterial community structure of burn patients was significantly altered compared with control patients. We determined that the unburned autologous donor skin from burn patients exhibits a microbiome similar to that of the burn margin, rather than unburned controls, and that changes in the cutaneous microbiome statistically correlate with several post-burn complications. We established that Corynebacterium positively correlated with burn wound infection, while Staphylococcus and Propionibacterium negatively correlated with burn wound infection. Both Corynebacterium and Enterococcus negatively correlated with the development of sepsis.

CONCLUSIONS

This study identifies distinct differences in the cutaneous microbiome between burn subjects and unburned controls, and ascertains that select bacterial taxa significantly correlate with several comorbid complications of burn injury. These preliminary data suggest that grafting donor skin exhibiting bacterial dysbiosis may augment infection and/or graft failure and sets the foundation for more in-depth and mechanistic analyses in presumably "healthy" donor skin from patients requiring skin grafting procedures.

Profiling microbial strains in urban environments using metagenomic sequencing data

Background

The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context. It is thus currently unclear whether such methods, that have proven successful at distinguishing even closely related strains in human microbiomes, are also effective in urban settings for tasks such as cultivation-free pathogen detection and microbial surveillance. Here, we aimed at a) testing the currently available metagenomic profiling tools on urban metagenomics; b) characterizing the organisms in urban environment at the resolution of single strain and c) discussing the biological insights that can be inferred from such methods.

Results

We applied three complementary methods on the 1614 metagenomes of the CAMDA 2017 challenge. With MetaMLST we identified 121 known sequence-types from 15 species of clinical relevance. For instance, we identified several Acinetobacter strains that were close to the nosocomial opportunistic pathogen A. nosocomialis. With StrainPhlAn, a generalized version of the MetaMLST approach, we inferred the phylogenetic structure of Pseudomonas stutzeri strains and suggested that the strain-level heterogeneity in environmental samples is higher than in the human microbiome. Finally, we also probed the functional potential of the different strains with PanPhlAn. We further showed that SNV-based and pangenome-based profiling provide complementary information that can be combined to investigate the evolutionary trajectories of microbes and to identify specific genetic determinants of virulence and antibiotic resistances within closely related strains.

Conclusion

We show that strain-level methods developed primarily for the analysis of human microbiomes can be effective for city-associated microbiomes. In fact, (opportunistic) pathogens can be tracked and monitored across many hundreds of urban metagenomes. However, while more effort is needed to profile strains of currently uncharacterized species, this work poses the basis for high-resolution analyses of microbiomes sampled in city and mass transportation environments.

Reviewers

This article was reviewed by Alexandra Bettina Graf, Daniel Huson and Trevor Cickovski.

Electronic supplementary material

The online version of this article (10.1186/s13062-018-0211-z) contains supplementary material, which is available to authorized users.

Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows

Eutrophication can play a significant role in seagrass decline and habitat loss. Microorganisms in seagrass sediments are essential to many important ecosystem processes, including nutrient cycling and seagrass ecosystem health. However, current knowledge of the bacterial communities, both beneficial and detrimental, within seagrass meadows in response to nutrient loading is limited. We studied the response of sediment bacterial and pathogen communities to nutrient enrichment on a tropical seagrass meadow in Xincun Bay, South China Sea. The bacterial taxonomic groups across all sites were dominated by the Gammaproteobacteria and Firmicutes. Sites nearest to the nutrient source and with the highest NH₄⁺ and PO₄³⁻ content had approximately double the relative abundance of putative denitrifiers Vibrionales, Alteromonadales, and Pseudomonadales. Additionally, the relative abundance of potential pathogen groups, especially Vibrio spp. and Pseudoalteromonas spp., was approximately 2‐fold greater at the sites with the highest nutrient loads compared to sites further from the source. These results suggest that proximity to sources of nutrient pollution increases the occurrence of potential bacterial pathogens that could affect fishes, invertebrates and humans. This study shows that nutrient enrichment does elicit shifts in bacterial community diversity and likely their function in local biogeochemical cycling and as a potential source of infectious diseases within seagrass meadows.

Diets Alter the Gut Microbiome of Crocodile Lizards

The crocodile lizard is a critically endangered reptile, and serious diseases have been found in this species in recent years, especially in captive lizards. Whether these diseases are caused by changes in the gut microbiota and the effect of captivity on disease remains to be determined. Here, we examined the relationship between the gut microbiota and diet and disease by comparing the fecal microbiota of wild lizards with those of sick and healthy lizards in captivity. The gut microbiota in wild crocodile lizards was consistently dominated by Proteobacteria (∼56.4%) and Bacteroidetes (∼19.1%). However, the abundance of Firmicutes (∼2.6%) in the intestine of the wild crocodile lizards was distinctly lower than that in other vertebrates. In addition, the wild samples from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve also had a high abundance of Deinococcus-Thermus while the wild samples from Guangxi Daguishan Crocodile Lizard National Nature Reserve had a high abundance of Tenericutes. The gut microbial community in loach-fed crocodile lizards was significantly different from the gut microbial community in the earthworm-fed and wild lizards. In addition, significant differences in specific bacteria were detected among groups. Notably, in the gut microbiota, the captive lizards fed earthworms resulted in enrichment of Fusobacterium, and the captive lizards fed loaches had higher abundances of Elizabethkingia, Halomonas, Morganella, and Salmonella, all of which are pathogens or opportunistic pathogens in human or other animals. However, there is no sufficient evidence that the gut microbiota contributes to either disease A or disease B. These results provide a reference for the conservation of endangered crocodile lizards and the first insight into the relationship between disease and the gut microbiota in lizards.

Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees

Gut microbiomes play crucial roles in animal health, and shifts in the gut microbial community structure can have detrimental impacts on hosts. Studies with vertebrate models and human subjects suggest that antibiotic treatments greatly perturb the native gut community, thereby facilitating proliferation of pathogens. In fact, persistent infections following antibiotic treatment are a major medical issue. In apiculture, antibiotics are frequently used to prevent bacterial infections of larval bees, but the impact of antibiotic-induced dysbiosis (microbial imbalance) on bee health and susceptibility to disease has not been fully elucidated. Here, we evaluated the effects of antibiotic exposure on the size and composition of honeybee gut communities. We monitored the survivorship of bees following antibiotic treatment in order to determine if dysbiosis of the gut microbiome impacts honeybee health, and we performed experiments to determine whether antibiotic exposure increases susceptibility to infection by opportunistic pathogens. Our results show that antibiotic treatment can have persistent effects on both the size and composition of the honeybee gut microbiome. Antibiotic exposure resulted in decreased survivorship, both in the hive and in laboratory experiments in which bees were exposed to opportunistic bacterial pathogens. Together, these results suggest that dysbiosis resulting from antibiotic exposure affects bee health, in part due to increased susceptibility to ubiquitous opportunistic pathogens. Not only do our results highlight the importance of the gut microbiome in honeybee health, but they also provide insights into how antibiotic treatment affects microbial communities and host health.

There is growing evidence for the importance of gut microbes in animal health. Unlike most other insects, honeybees possess a highly conserved gut microbial community, which is acquired through social contact, and several results have suggested that these microbes play an important role in honeybee health. Antibiotics, which can severely disrupt gut microbial communities, are commonly used in beekeeping in several countries. However, it is unknown how antibiotic treatment affects the gut microbial communities of honeybees. Here, we evaluated the effects of antibiotic treatment on the size and composition of the honeybee gut microbiome and on honeybee health. We found that exposure to antibiotics significantly alters the honeybee gut microbial community structure and leads to decreased survivorship of honeybees in the hive, likely due to increased susceptibility to infection by opportunistic pathogens.

Peritoneal dialysis-related peritonitis due to Halomonas hamiltonii: A first case report

INTRODUCTION

Halomonas hamiltonii is a Gram-negative, halophilic, motile, and nonspore-forming rod bacterium. Although most Halomonas sp. are commonly found in saline environments, it has rarely been implicated as a cause of human infection. Herein, the authors present a case report of continuous ambulatory peritoneal dialysis (CAPD)-related peritonitis attributed to H hamiltonii.

CASE PRESENTATION

An 82-year-old male patient who had been receiving CAPD therapy presented to an emergency department with complaints of abdominal pain and cloudy dialysate that had persisted for 2 days. The peritoneal dialysate was compatible with CAPD peritonitis, with white blood cell count of peritoneal effluent of 810/mm and neutrophils predominated (60%). Two days after culture on blood agar medium, nonhemolytic pink mucoid colonies showed, with cells showing Gram-negative, nonspore-forming rods with a few longer and larger bacilli than usual were found. We also performed biochemical tests and found negative responses in K/K on the triple sugar iron test and H2S and equivocal (very weak) response in the motility test, but positive responses to catalase, oxidase, and urease tests. The partial sequence of the 16S rRNA gene of a bacterium detected by peritoneal fluid culture was utilized for a Basic Local Alignment Search Tool search, which revealed that the organism was H hamiltonii. Intraperitoneal antibiotics were administered for 21 days, and the patient was discharged without clinical problems.

CONCLUSION

We present here the first case report of CAPD-related peritonitis caused by H hamiltonii, which was identified using molecular biological techniques. Although guidelines do not exist for the treatment of infections caused by this organism, conventional treatment for Gram-negative organisms could be effective.

Lipid Emulsion Formulation of Parenteral Nutrition Affects Intestinal Microbiota and Host Responses in Neonatal Piglets

BACKGROUND

Total parenteral nutrition (TPN) is a cause of intestinal microbial dysbiosis and impaired gut barrier function. This may contribute to life-threatening parenteral nutrition-associated liver disease and sepsis in infants. We compared the effects of a lipid emulsion containing long-chain ω-3 polyunsaturated fatty acids (PUFAs; SMOFlipid) and a predominantly ω-6 PUFA emulsion (Intralipid) on microbial composition and host response at the mucosal surface.

MATERIALS AND METHODS

Neonatal piglets were provided isocaloric, isonitrogenous TPN for 14 days versus sow-fed (SF) controls. Equivalent lipid doses (10 g/kg/d) were given of either SMOFlipid (ML; n = 10) or Intralipid (SO; n = 9). Ileal segments and mucosal scrapings were used to characterize microbial composition by 16S rRNA gene sequencing and quantitative gene expression of tight junction proteins, mucins, antimicrobial peptides, and inflammatory cytokines.

RESULTS

The microbial composition of TPN piglets differed from SF, while ML and SO differed from each other (analysis of molecular variance; P < .05); ML piglets were more similar to SF, as indicated by UniFrac distance ( P < .05). SO piglets showed a specific and dramatic increase in Parabacteroides ( P < .05), while ML showed an increase in Enterobacteriaceae ( P < .05). Gene expression of mucin, claudin 1, β-defensin 2, and interleukin 8 were higher in TPN; overall increases were significantly less in ML versus SO ( P < .05).

CONCLUSION

The formulation of parenteral lipid is associated with differences in the gut microbiota and host response of TPN-fed neonatal piglets. Inclusion of ω-3 long-chain PUFAs appears to improve host-microbial interactions at the mucosal surface, although mechanisms are yet to be defined.

Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors

Vector-borne microbes are subject to the ecological constraints of two distinct microenvironments: that in the arthropod vector and that in the blood of its vertebrate host. Because the structure of bacterial communities in these two microenvironments may substantially affect the abundance of vector-borne microbes, it is important to understand the relationship between bacterial communities in both microenvironments and the determinants that shape them. We used pyrosequencing analyses to compare the structure of bacterial communities in Synosternus cleopatrae fleas and in the blood of their Gerbillus andersoni hosts. We also monitored the interindividual and seasonal variability in these bacterial communities by sampling the same individual wild rodents during the spring and again during the summer. We show that the bacterial communities in each sample type (blood, female flea or male flea) had a similar phylotype composition among host individuals, but exhibited seasonal variability that was not directly associated with host characteristics. The structure of bacterial communities in male fleas and in the blood of their rodent hosts was remarkably similar and was dominated by flea-borne Bartonella and Mycoplasma phylotypes. A lower abundance of flea-borne bacteria and the presence of Wolbachia phylotypes distinguished bacterial communities in female fleas from those in male fleas and in rodent blood. These results suggest that the overall abundance of a certain vector-borne microbe is more likely to be determined by the abundance of endosymbiotic bacteria in the vector, abundance of other vector-borne microbes co-occurring in the vector and in the host blood and by seasonal changes, than by host characteristics.

Microbiology and epidemiology of Halomonas species

Halomonas has been organized as a genus since 1980, and comprises halophilic and/or halotolerant Gram-negative aerobic bacteria, typically found in saline environments. The genus is enlarging: at present, 76 species are taxonomically recognized, with more to be added. Increasing industrial uses have been found, largely in bioremediation and the production of desirable compounds. Originally seen as environmental contaminants, pathogenicity was initially not recognized; however, disease in algae, animals and humans has now been described. As the biotechnological use of these species increases, and the ability to isolate and recognize them improves, one might expect further pathogenic encounters with humans to be described.

Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome

Functional environmental screening of metagenomic libraries is a powerful means to identify and assign function to novel genes and their encoded proteins without any prior sequence knowledge. In the current study we describe the identification and subsequent analysis of a salt-tolerant clone from a human gut metagenomic library. Following transposon mutagenesis we identified an unknown gene (stlA, for “salt tolerance locus A”) with no current known homologues in the databases. Subsequent cloning and expression in Escherichia coli MKH13 revealed that stlA confers a salt tolerance phenotype in its surrogate host. Furthermore, a detailed in silico analysis was also conducted to gain additional information on the properties of the encoded StlA protein. The stlA gene is rare when searched against human metagenome datasets such as MetaHit and the Human Microbiome Project and represents a novel and unique salt tolerance determinant which appears to be found exclusively in the human gut environment.

Perturbation of the indigenous rat oral microbiome by ciprofloxacin dosing

Mucosal surfaces such as the gut, vagina and oral cavity are colonized by microbiota that are an integral component of the healthy ecosystem. Recent molecular techniques make it feasible to correlate antimicrobial dosing levels with changes in microbiome composition. The objective of this study was to characterize the rat oral plaque microbiome composition at doses of ciprofloxacin that were considerably above and below nominal in vitro minimal inhibitory concentrations of a variety of gram-positive oral commensal bacteria. We exposed the oral cavities of rats to relatively low (0.1 μg ml(-1) ) and high (20 μg ml(-1)) doses of ciprofloxacin in the drinking water over a 3-day period. Plaque microbiota were characterized using 454 pyrosequencing. The rat indigenous community was dominated by the genera Rothia (74.4%) and Streptococcus (4.7%). Dosing at 0.1 μg ml(-1) was associated with changes in Rothia and Streptococcus species that were not significant, whereas dosing at 20 μg ml(-1) caused a pronounced (significant) reduction in the relative abundance of the Streptococcus genus. Taxonomic independent analysis indicated that the perturbation in the overall community structure attributed to dosing with ciprofloxacin at either the low or high dose was relatively low. The results suggest that it is feasible to use an antimicrobial dosing regimen to selectively target a specific subset of a mucosal microbiome for elimination with minimal perturbation of the entire community.

Halomonas johnsoniae: review of a medically underappreciated genus of growing human importance

The growing genus Halomonas includes bacteria favoring or tolerating high-saline/halide and high-pH environments. Infections are rarely reported. A patient developed Halomonas johnsoniae (previously reported only as dialysis unit environmental contaminants) bacteremia. The medical community is alerted to the pathogenic potential of the genus, particularly in a dialysis setting.

Draft genome sequence of the human pathogen Halomonas stevensii S18214T

Halomonas stevensii is a Gram-negative, moderately halophilic bacterium causing environmental contamination and infections in a dialysis center. Here we present the 3.7-Mb draft genome sequence of the type strain (S18214(T)) of H. stevensii, which will give insight into the pathogenic potential of H. stevensii.

Growth of Dunaliella tertiolecta and associated bacteria in photobioreactors

The aim of this study was to test three flat-plate photobioreactor configurations for cultivation of marine green alga Dunaliella tertiolecta under non-axenic growth conditions and to characterize and quantify the associated bacteria. The photobioreactor cultivations were conducted using tap water-based media. Static mixers intended to enhance mixing and light utilization did not generally increase algal growth at the low light intensities used. The maximum biomass concentration (measured as volatile suspended solids) and maximum specific growth rate achieved in the flat plate with no mixer were 2.9 g l⁻¹ and 1.3 day⁻¹, respectively. Based on quantitative polymerase chain reaction, bacterial growth followed the growth of D. tertiolecta. Based on 16S rDNA amplification and denaturing gradient gel electrophoresis profiling, heterotrophic bacteria in the D. tertiolecta cultures mainly originated from the non-axenic algal inocula, and tap water heterotrophs were not enriched in high chloride media (3 % salinity). Bacterial communities were relatively stable and reproducible in all flat-plate cultivations and were dominated by Gammaproteobacteria, Flavobacteria, and Alphaproteobacteria.

Multilocus sequence analysis of the family Halomonadaceae

Multilocus sequence analysis (MLSA) protocols have been developed for species circumscription for many taxa. However, at present, no studies based on MLSA have been performed within any moderately halophilic bacterial group. To test the usefulness of MLSA with these kinds of micro-organisms, the family Halomonadaceae, which includes mainly halophilic bacteria, was chosen as a model. This family comprises ten genera with validly published names and 85 species of environmental, biotechnological and clinical interest. In some cases, the phylogenetic relationships between members of this family, based on 16S rRNA gene sequence comparisons, are not clear and a deep phylogenetic analysis using several housekeeping genes seemed appropriate. Here, MLSA was applied using the 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA genes for species of the family Halomonadaceae. Phylogenetic trees based on the individual and concatenated gene sequences revealed that the family Halomonadaceae formed a monophyletic group of micro-organisms within the order Oceanospirillales. With the exception of the genera Halomonas and Modicisalibacter, all other genera within this family were phylogenetically coherent. Five of the six studied genes (16S rRNA, 23S rRNA, gyrB, rpoD and secA) showed a consistent evolutionary history. However, the results obtained with the atpA gene were different; thus, this gene may not be considered useful as an individual gene phylogenetic marker within this family. The phylogenetic methods produced variable results, with those generated from the maximum-likelihood and neighbour-joining algorithms being more similar than those obtained by maximum-parsimony methods. Horizontal gene transfer (HGT) plays an important evolutionary role in the family Halomonadaceae; however, the impact of recombination events in the phylogenetic analysis was minimized by concatenating the six loci, which agreed with the current taxonomic scheme for this family. Finally, the findings of this study also indicated that the 16S rRNA, gyrB and rpoD genes were the most suitable genes for future taxonomic studies using MLSA within the family Halomonadaceae.

Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic

A Gram-negative, heterotrophic, aerobic, non-endospore-forming, peritrichously flagellated and motile bacterial strain, designated BH1T, was isolated from samples of rusticles, which are formed in part by a consortium of micro-organisms, collected from the RMS Titanic wreck site. The strain grew optimally at 30–37 °C, pH 7.0–7.5 and in the presence of 2–8 % (w/v) NaCl. We carried out a polyphasic taxonomic study in order to characterize the strain in detail. Phylogenetic analyses based on 16S rRNA gene sequence comparison indicated that strain BH1T clustered within the branch consisting of species of Halomonas. The most closely related type strains were Halomonas neptunia (98.6 % 16S rRNA sequence similarity), Halomonas variabilis (98.4 %), Halomonas boliviensis (98.3 %) and Halomonas sulfidaeris (97.5 %). Other closely related species were Halomonas alkaliphila (96.5 % sequence similarity), Halomonas hydrothermalis (96.3 %), Halomonas gomseomensis (96.3 %), Halomonas venusta (96.3 %) and Halomonas meridiana (96.2 %). The major fatty acids of strain BH1T were C18 : 1 ω7c (36.3 %), C16 : 0 (18.4 %) and C19 : 0 cyclo ω8c (17.9 %). The DNA G+C content was 60.0 mol% (T m). Ubiquinone 9 (Q-9) was the major lipoquinone. The phenotypic features, fatty acid profile and DNA G+C content further supported the placement of strain BH1T in the genus Halomonas. DNA–DNA hybridization values between strain BH1T and H. neptunia CECT 5815T, H. variabilis DSM 3051T, H. boliviensis DSM 15516T and H. sulfidaeris CECT 5817T were 19, 17, 30 and 29 %, respectively, supporting the differential taxonomic status of BH1T. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain BH1T is considered to represent a novel species, for which the name Halomonas titanicae sp. nov. is proposed. The type strain is BH1T (=ATCC BAA-1257T =CECT 7585T =JCM 16411T =LMG 25388T).

O-chain structure from the lipopolysaccharide of the human pathogen Halomonas stevensii strain S18214

Halomonas stevensii is a Gram-negative, pathogenic, moderately halophilic bacterium isolated from the blood of a renal care patient. It optimally grows at 30-35°C at pH 8-9 and at a sea salt concentration ranging from 3.0% to 7.5%. Gram-negative bacterial infections are closely associated with the presence of the lipopolysaccharides (LPSs) on the outer membrane. These molecules consist of three regions covalently linked: the glycolipid (lipid A), the oligosaccharide region (core region), and the O-specific polysaccharide (O-chain, O-antigen). O-antigen seems to play an important role in the colonization step (adherence) and the ability to bypass host defense mechanisms. For this reason the structure elucidation of the O-chain repeating unit is important to improve knowledge about the role of LPS in the host-pathogen interaction. In this paper, we report the complete structure of the O-chain from the LPS of H. stevensii. The bacterial cells were cultivated and LPS was extracted by the PCP (phenol-chloroform-petroleum ether) method. After mild acid hydrolysis, the lipid A was removed by centrifugation and the obtained polysaccharide was analyzed by means of chemical analysis and one- and two-dimensional NMR spectroscopy giving the following structure: