Rare Bacteria Research Articles

Rare Bacteria Assembly in Soils Is Mainly Driven by Deterministic Processes.

Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules.

Environmental adaptation is stronger for abundant rather than rare microorganisms in wetland soils from the Qinghai-Tibet Plateau.

Disentangling the biogeographic patterns of rare and abundant microbes is essential in order to understand the generation and maintenance of microbial diversity with respect to the functions they provide. However, little is known about ecological assembly processes and environmental adaptation of rare and abundant microbes across large spatial-scale wetlands. Using Illumina sequencing and multiple statistical analyses, we characterized the taxonomic and phylogenetic diversity of rare and abundant bacteria and fungi in Qinghai-Tibet Plateau wetland soils. Abundant microbial taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological traits than rare ones. By contrast, rare taxa showed higher sensitivity to environmental changes and closer phylogenetic clustering than abundant ones. The null model analysis revealed that dispersal limitation belonging to stochastic process dominated community assemblies of abundant bacteria, and rare and abundant fungi, while variable selection belonging to deterministic process governed community assembly of rare bacteria. Neutral model analysis and variation partitioning analysis further confirmed that abundant microbes were less environmentally constrained. Soil ammonia nitrogen was the crucial factor in mediating the balance between stochasticity and determinism of both rare and abundant microbes. Abundant microbes may have better environmental adaptation potential and are less dispersed by environmental changes than rare ones. Our findings extend knowledge of the adaptation of rare and abundant microbes to ongoing environmental change and could facilitate prediction of biodiversity loss caused probably by climate change and human activity in the Qinghai-Tibet Plateau wetlands.

Assembly of abundant and rare bacterial and fungal sub-communities in different soil aggregate sizes in an apple orchard treated with cover crop and fertilizer

Soil bacterial and fungal communities often comprise the “abundant biosphere” and “rare biosphere”, which co-exist in soil aggregates to form a complex system of inter-species interactions. However, the different assembly processes exhibited by abundant and rare bacterial and fungal communities due to the spatial isolation of aggregates are still unclear. In this study, the stochastic and deterministic processes associated with the assembly of abundant and rare sub-communities of bacteria and fungi were quantified in different sized soil aggregates in apple orchards treated with a cover crop and fertilizer. The importance of variable selection in the assembly of the abundant bacterial community increased from macroaggregates to small microaggregates. The assembly of the rare bacterial community followed a transition from homogeneous selection to weak homogeneous selection with decreases in the soil organic carbon and total nitrogen contents. Both the abundant and rare bacterial community assemblies in soil aggregates were not limited in terms of their dispersal. The assembly of the abundant fungal community was dominated by stochastic processes, whereas the assembly of the rare fungal community was dominated by homogeneous selection and limited dispersal in different sized soil aggregates. The compositions of the abundant and rare bacterial and fungal communities were also affected by soil aggregates and agricultural practices. Most of the top 20 operational taxonomic units (OTUs) with high abundances among bacteria and fungi were related to the macroaggregate amounts compared with rare bacteria and fungi, and some OTUs among abundant fungi were related to the microaggregate and small microaggregate amounts. This study provides a priori hypotheses for testing in future experiments, thereby facilitating a systematic approach to understand the mechanisms responsible for the changes in the fungal and bacterial community compositions in different sized soil aggregates.

Nationwide surveillance reveals frequent detection of carbapenemase-producing Enterobacterales in Dutch municipal wastewater

Carbapenemase-producing Enterobacterales (CPE) pose a threat to public health necessitating restriction of further spread. Tools to efficiently monitor the prevalence of these still relatively rare resistant bacteria and insight in routes of dissemination are pivotal for the development of prevention strategies. By analysis of untreated and treated wastewater from 100 municipal wastewater treatment plants (WWTPs) together serving over 40% of the Dutch population, this study investigated both the distribution of CPE in the Dutch population, and WWTPs as a source of CPE in the aquatic environment.CPE were detected at 89% of the WWTPs, in 87 influents and 53 effluents. Overall, 15 different CPE-types were detected based on species and carbapenemase gene. The most widely distributed were E. coli carrying blaOXA-48-like genes, which were detected at 88 WWTPs including small WWTPs without connected health care institutions (HCI). BlaOXA-48-like-positive-K. pneumoniae, blaNDM- or blaKPC-positive E. coli, and blaNDM- or blaKPC-positive K. pneumoniae were detected at 33, 20, and 14 WWTPs, respectively. Mean influent and effluent CPE concentrations were 7.9×102 cfu/l and 11 cfu/l. The total daily number of CPE discharged by the 100 WWTPs was estimated to be 2.2×1011 cfu. In multivariate analysis, CPE concentrations in untreated wastewater were positively associated with WWTP size and E. coli concentrations, but not with the presence of HCI. Based on the total number of CPE (9.7×1012 cfu) and ESBL-E. coli (2.41015 cfu) in influents, and a prevalence of approximately 5% in the Dutch population for ESBL-E. coli, the prevalence of CPE in the Dutch population was roughly estimated to be 0.02%.Wastewater surveillance is an efficient tool to monitor the distribution of CPE in the population at a national level and may supplement human surveillance data. CPE are emitted to the aquatic environment with treated wastewater and associated public health risks need to be determined.

Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau.

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3–V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

Microbial diversity of co-occurring heterotrophs in cultures of marine picocyanobacteria

BackgroundThe cyanobacteria Prochlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; heterotrophs grow on organic carbon supplied by the photolithoautotrophs. For examining the selective pressures shaping autotroph/heterotroph interactions, we have made use of unialgal enrichment cultures of Prochlorococcus and Synechococcus maintained for hundreds to thousands of generations in the lab. We examine the diversity of heterotrophs in 74 enrichment cultures of these picocyanobacteria obtained from diverse areas of the global oceans.ResultsHeterotroph community composition differed between clades and ecotypes of the autotrophic ‘hosts’ but there was significant overlap in heterotroph community composition across these cultures. Collectively, the cultures were comprised of many shared taxa, even at the genus level. Yet, observed differences in community composition were associated with time since isolation, location, depth, and methods of isolation. The majority of heterotrophs in the cultures are rare in the global ocean, but enrichment conditions favor the opportunistic outgrowth of these rare bacteria. However, we found a few examples, such as bacteria in the family Rhodobacteraceae, of heterotrophs that were ubiquitous and abundant in cultures and in the global oceans. We found their abundance in the wild is also positively correlated with that of picocyanobacteria.ConclusionsParticular conditions surrounding isolation have a persistent effect on long-term culture composition, likely from bottlenecking and selection that happen during the early stages of enrichment for the picocyanobacteria. We highlight the potential for examining ecologically relevant relationships by identifying patterns of distribution of culture-enriched organisms in the global oceans.

Composition and co-occurrence network of the rhizosphere bacterial community of two emergent macrophytes and implications for phytoremediation

Microorganisms of the rhizosphere play essential roles in plant metabolism, growth and productivity. Phragmites australis and Triarrhena lutarioriparia are two commonly found emergent macrophytes of the Gramineae family. P. australis is widely used in constructed or artificial wetlands, whereas T. lutarioriparia is found in natural environments. Thus, these two macrophytes have different ecological functions within aquatic ecosystems. In this study we used 16S rRNA gene-based high-throughput sequencing to compare the diversity, composition and co-occurrence networks of the rhizosphere bacterial communities of each macrophyte to better understand their respective ecological functions. The results suggested that abundant taxa in the bacterial communities had a higher richness and were more diverse in the bulk soil relative to the rhizosphere compartment. The opposite pattern was found for rare bacteria in the respective microbial communities. The bacterial rhizosphere community of P. australis contained a greater proportion of genera associated with purifying water and improving water quality than that of T. lutarioriparia. P. australis also had a more complex rhizosphere bacterial network than T. lutarioriparia. These findings provide a better understanding of the ecological functions of the two macrophytes and show that adjusting plant–bacteria interactions within the macrophyte rhizosphere community is an important aspect of phytoremediation.

Bacterial profiling of head lice isolated from the Orang Asli: A first report in Malaysia

This study was carried out to determine from bacterial profiling to the bacterial profiles of head lice among the Orang Asli communities. The head lice were collected from Orang Asli community volunteers. The surface sterilized head lice pools were subjected to genomic DNA extraction while next generation sequencing of the 16S rRNA gene was performed using the Illumina MiSeq platform. Six female and three male head lice identified as Pediculus humanus capitis were collected. A total of 111 368 number of NGS sequencing reads were recorded while another 223 bacterial taxa sequences were obtained. Symbiotic bacteria showed the highest number of reads, with Arsenophonus and Rhodococcus sequences being the most abundant genera in the female and male samples, respectively. The female head lice contained a more distinct microbial diversity. Amongst the pathogenic bacterial species sequences noted were the methicillin-resistant Staphylococcus aureus, Streptobacillus moniliformis, Haemophilus influenzae, Bordetella pertussis and Acinetobacter baumannii. The 16S rRNA genome sequencing revealed a number of rare and pathogenic bacterial species within the head lice of the Orang Asli. The socio-economic practices of the community which involved forest foraging and hunting, and their poor living conditions potentially facilitated the transmission of zoonotic bacterial pathogens, including those found within the head lice. Hence, there is the possibility that the head lice could serve as vectors for the transmission of pathogenic bacteria. This study highlighted the diverse microbial community found within the head lice's gut of the Orang Asli, with the detection of multiple rare and pathogenic bacteria capable of causing severe infections.

Distinct Community Assembly Processes of Abundant and Rare Soil Bacteria in Coastal Wetlands along an Inundation Gradient.

Microbial communities commonly consist of a large number of rare taxa (RT) and few abundant taxa (AT), and it is important to identify the differences of the community assembly processes between RT and AT in response to environmental changes. However, the community assembly processes governing AT and RT in coastal wetland soils along an inundation gradient remain elusive. Here, an in situ mesocosm, with continuous inundation gradients and native mangrove Kandelia obovata or exotic cordgrass Spartina alterniflora, was established to determine the patterns and driving factors of community turnover and assembly processes of AT and RT. We found that RT exhibited a remarkably lower turnover rate than AT, and the niche breadth of RT was significantly narrower than that of AT. In comparison with AT, RT presented stronger phylogenetic signals for ecological preferences across environmental gradients. Null model analyses revealed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Soil water content was the most decisive factor for community turnover and assembly processes of both AT and RT. Structural equation modeling analysis showed that RT were strongly associated with K. obovata biomass rather than S. alterniflora biomass, suggesting a strong relationship between RT and the growth of mangrove K. obovata Overall, our study revealed distinct assembly processes of soil AT and RT communities in coastal wetlands, which is crucial for mechanistic understanding of the establishment and maintenance of soil microbial diversity in coastal wetlands under conditions of global environmental changes.IMPORTANCE Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). In this study, we found that RT exhibited narrower niche breadth and stronger phylogenetic signals than AT. Null model analyses showed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Revealing the differences in the community assembly processes between AT and RT in coastal wetlands is critical to understand the establishment and maintenance of soil microbial diversity in coastal wetlands with regard to environmental changes.

Characterization of gut microbiota associated with clinical parameters in intrahepatic cholestasis of pregnancy

BackgroundIntrahepatic cholestasis of pregnancy (ICP) is a liver disorder that specifically occurs in pregnancy. Elevated levels of liver transaminases aspartate aminotransferase, alanine aminotransferase and serum bilirubin levels are common biochemical characteristics in ICP. The disorder is associated with an increased risk of premature delivery and stillbirth. The characterization of the potential microbiota in ICP could go a long way in the prevention and treatment of this pregnancy disease.MethodsA total of 58 patients were recruited for our study: 27 ICP patients and 31 healthy pregnant subjects with no ICP. The V3 and V4 regions of the 16S rDNA collected from fecal samples of both diseased and control groups were amplified. 16S rRNA gene amplicon sequencing was then performed on gut microbiota. Sequencing data were analyzed and the correlation between components of microbiota and patient ICP status was found. Related metabolic pathways, relative abundance and significantly different operational taxonomic units (OTUs) between ICP and controls were also identified.ResultsElevated levels of total bile acid, ALT, AST, Dbil and Tbil were recorded or observed in ICP subjects as compared to the control. Gut microbiota in pregnant women was dominated by four major phyla and 27 core genera. PCoA analysis results indicated that there was no significant clustering in Bray–Curtis distance matrices. Our results showed that there was a correlation between specific OTUs and measured clinical parameters of pregnant women. Comparison at the different taxonomy levels revealed high levels of abundance of Blautia and Citrobacter in ICP patients. At the family level, Enterobacteriaceae and Leuconostocaceae were higher in ICP patients. 638 KEGG Orthologs and 138 pathways significantly differed in the two groups. PLS-DA model with VIP plots indicated a total of eight genera and seven species were key taxa in ICP and control groups.ConclusionsOur research indicated that although there was no significant clustering by PCoA analysis, patients with ICP have increased rare bacteria at different phylogenetic levels. Our results also illustrated that all 638 KEGG Orthologs and 136 in 138 KEGG pathways were less abundant in ICP patients compared to the controls.

Differential response of abundant and rare bacterial subcommunities to abiotic and biotic gradients across temperate deserts

The biogeography of soil bacterial communities has been well documented, yet the associated difference in spatial distribution and drivers between abundant and rare bacteria still remains unclear. Here, we compared the species richness, composition, and their drivers of rare and abundant bacteria along a 2500-km regional transect in Chinese deserts. Our results demonstrated that abundant and rare bacterial diversities were determined by plant community together with climatic, soil and spatial factors, but the shifts in bacterial richness and composition caused by abiotic and biotic variations varied between abundant and rare subcommunities. Rare bacterial richness significantly decreased with increasing temperature, drought and nutrient limitation, while abundant bacterial richness showed an increasing trend. Plant richness was negatively associated with abundant bacterial richness, but positively related to rare bacterial richness. Abiotic and biotic differences caused greater variations in rare species composition than that in abundant species composition. Furthermore, our results also confirmed that the spatial patterns of abundant and rare bacterial distribution differed remarkably. Our findings collectively suggest that similar abiotic and biotic drivers but distinct influences lead to distinct spatial distribution patterns of abundant and rare bacteria in harsh deserts. Therefore, taking more ecological traits such as stress tolerance and abundance into account will strengthen our understanding of soil bacterial assembly mechanisms.

Suspicion of epizootic Lawsonia intracellularis disease in a group of pileated gibbons (Hylobates pileatus)

Within a month, all five individuals of a pileated gibbon (Hylobates pileatus) family presented the same symptoms: diarrhoea, vomiting and severe apathy. During this first outbreak, three of them died...

Vogesella perlucida-induced bacteremia in an advanced-age patient: first case report

BackgroundVogesella species are common aquatic, Gram-negative rod-shaped bacteria, originally described in 1997. Vogesella perlucida was first isolated from spring water in 2008. Furthermore, bacterial pathogenicity of Vogesella perlucida has never been reported. Here, we report the first case of rare Vogesella perlucida-induced bacteremia in an advanced-age patient with many basic diseases and history of dexamethasone abuse.Case presentationA 71-year-old female was admitted with inflamed upper and lower limbs, rubefaction, pain and fever (about 40 °C). She had been injured in a fall at a vegetable market and then touched river snails with her injury hands. A few days later, soft tissue infection of the patient developed and worsened. Non-pigmented colonies were isolated from blood cultures of the patient. Initially, Vogesella perlucida was wrongly identified as Sphingomonas paucimobilis by Vitek-2 system with GN card. Besides, we failed to obtain an acceptable identification by the MALDI-TOF analysis. Finally, the isolated strain was identified as Vogesella perlucida by 16S rRNA gene sequences. In addition, the patient recovered well after a continuous treatment of levofloxacin for 12 days.ConclusionTraditional microbiological testing system may be inadequate in the diagnosis of rare pathogenic bacteria. Applications of molecular diagnostics techniques have great advantages in clinical microbiology laboratory. By using 16S rRNA gene sequence analysis, we report the the first case of rare Vogesella perlucida-induced bacteremia.

Articulation coxo-fémorale et grossesse

One third of pregnant women can complain of the hip, but other sources of pain must first be ruled out: spine, sacroiliac, pubis, pelvis, trochanter, and tendons (including gluteus minus). Entrapment of lateral cutaneous and obturator nerves should not be forgotten. Once a coxo-femoral origin is ascertained, the most frequent diagnosis might be labral stresses or tears, although a high percentage of false negative on imaging often preclude a firm diagnosis. Septic arthritis are very rare but unusual bacteria like streptococcus B can be noticed. MRI must be requested each time hip pain or limping is lasting enough, first to seek for stress fractures with or without underlying osteopenia, since they can progress to displaced fractures or osteonecrosis leading to hip prosthesis following delivery. Several mechanisms could co-exist to account for the underlying hip osteopenia: 1-pregnancy-related transient osteoporosis (which mainly induces multiple vertebral fractures); 2-algodystrophy (more often unilateral as compared to other explanations of hip osteopenia); oedema of the femoral neck and/or epiphysis, or full-blown osteonecrosis, possibly fostered by venous stasis secondary to compression by the foetus of maternal large veins in the pelvis. Previous hip prostheses have no influence on pregnancy outcome, and later children health, although abnormal levels of cobalt and chromium are usually found in their cord blood.

CTX-M-9 group ESBL-producing Raoultella planticola nosocomial infection: first report from sub-Saharan Africa

BackgroundRaoultella are Gram-negative rod-shaped aerobic bacteria which grow in water and soil. They mostly cause nosocomial infections associated with surgical procedures. This case study is the first report of a Raoultella infection in Africa.Case presentationWe report a case of a surgical site infection (SSI) caused by Raoultella planticola which developed after caesarean section (CS) and surgery for secondary small bowel obstruction. The patient became febrile with neutrophilia (19,157/µL) 4 days after laparotomy and started to develop clinical signs of a SSI on the 8th day after laparotomy. The patient continued to be febrile and became critically ill despite empirical treatment with ceftriaxone and vancomycin. Raoultella species with extended antimicrobial resistance (AMR) carrying the CTX-M-9 β-lactamase was isolated from the wound discharge. Considering the antimicrobial susceptibility test, ceftriaxone was replaced by ceftazidime. The patient recovered and could be discharged on day 29 after CS.ConclusionsRaoultella planticola was isolated from an infected surgical site after repeated abdominal surgery. Due to the infection the patient’s stay in the hospital was prolonged for a total of 4 weeks. It is noted that patients undergoing surgical and prolonged inpatient treatment are at risk for infections caused by Raoultella. The development of a SSI caused by Raoultella planticola with extended AMR has to be assumed to be a consequence of ineffective antibiotic utilization. The presented case advices that rare bacteria as Raoultella should be considered as potential cause of nosocomial SSI with challenging treatment due to high levels of AMR.

Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa.

To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3–V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.

Antibiotic-induced role interchange between rare and predominant bacteria retained the function of a bacterial community for denitrifying quinoline degradation.

Quinoline is a recalcitrant pollutant in coking wastewater which has been broadly investigated with many isolates possessing aerobic quinoline-degrading ability. However, studies on anaerobic degradation and the corresponding bacteria are very scarce. This study attempted to investigate the role of diverse functional members and the redundancy of quinoline degradation in a lab-scale quinoline denitrifying bioreactor. Antibiotics were added to the batch culture under denitrifying conditions to disturb the microbial community of the quinoline-degrading bioreactor. According to the results, the nitrate removal rate remained stable, and the quinoline removal rate increased by 9·7% after treatment with streptomycin. However, PCoA analysis of 16S rRNA gene sequencing data of these samples indicated a significant shift in microbial community structures. Specifically, 12 operational taxonomic units (OTUs), including OTU1 (Pseudomonas) and OTU2 (Achromobacter), were significantly enriched. OTU1 replaced OTU8 (Thauera) as the most predominant denitrifying quinoline-degrading member. However, OTU8 and other predominant OTUs (Comamonas and Pseudoxanthomonas), which were hypothesized to contribute essentially to quinoline degradation in the origin bioreactor, became almost undetectable. Functional redundancy due to high biological diversity allowed the role reversal of predominant quinoline-degrading bacteria and other rare bacteria when disturbed by antibiotic stress. Although the abundance of OTU1 was much lower initially, it replaced the essential role of the predominant member OTU8 in the bioreactor community for quinoline degradation once the environmental condition changed. This study indicated that the high biological diversity in a wastewater treatment bacterial community is crucial for maintaining the degrading function of organic pollutants, especially in a changing environment due to external disturbance or stress.

Molecular Mechanisms of Intercellular Dissemination of Bacterial Pathogens.

Several intracellular bacterial pathogens, including Listeria monocytogenes, Shigella flexerni, and Rickettsia spp. use an actin-based motility process to spread in mammalian cell monolayers. Cell-to-cell spread is mediated by protrusive structures that contain bacteria encased in the host cell plasma membrane. These protrusions, which form in infected host cells, are internalized by neighboring cells. In this review, we summarize key findings on cell-to-cell spread, focusing on recent work on mechanisms of protrusion formation and internalization. We also discuss the dynamic behavior of bacterial populations during spread, and highlight recent findings showing that intercellular spread by an extracellular bacterial pathogen.

Strategies for culturing active/dormant marine microbes.

Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However, many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture, there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for 'unculturable microbes' and categorizes uncultured bacteria into three groups: dominant active bacteria, rare active bacteria, and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria. Simulating the natural environment is an effective strategy for isolating dominant active bacteria, whereas culturomics and enrichment culture methods are proposed for isolating rare active bacteria. For dormant bacteria, resuscitation culture is an appropriate strategy. Furthermore, the review provides a list of the most-wanted bacteria and proposes potential strategies for culturing these bacteria in marine environments. The review provides new insight into the development of strategies for the cultivation of specific groups of uncultured bacteria and therefore paves the way for the detection of novel microbes and their functions in marine ecosystems.

Cultivation of Diverse and Rare Bacteria from the Human Gut Microbiome

Cultivation of Diverse and Rare Bacteria from the Human Gut Microbiome