Fusobacteria: new taxonomy and related diseases

Nanoplastic pollution changes the intestinal microbiome but not the morphology or behavior of a freshwater turtle

Humans produce 350 million metric tons of plastic waste per year, leading to microplastic pollution and widespread environmental contamination, particularly in aquatic environments. This subsequently impacts aquatic organisms in myriad ways, yet the vast majority of research is conducted in marine, rather than freshwater systems. In this study, we exposed eggs and hatchlings of the Chinese soft-shelled turtle (Pelodiscus sinensis) to 80-nm polystyrene nanoplastics (PS-NPs) and monitored the impacts on development, behavior and the gut microbiome. We demonstrate that 80-nm PS-NPs can penetrate the eggshell and move into developing embryos. This led to metabolic impairments, as evidenced by bradycardia (a decreased heart rate), which persisted until hatching. We found no evidence that nanoplastic exposure affected hatchling morphology, growth rates, or levels of boldness and exploration, yet we discuss some potential caveats here. Exposure to nanoplastics reduced the diversity and homogeneity of gut microbiota in P. sinensis, with the level of disruption correlating to the length of environmental exposure (during incubation only or post-hatching also). Thirteen core genera (with an initial abundance >1 %) shifted after nanoplastic treatment: pathogenic bacteria increased, beneficial probiotic bacteria decreased, and there was an increase in the proportion of negative correlations between bacterial genera. These changes could have profound impacts on the viability of turtles throughout their lives. Our study highlights the toxicity of environmental NPs to the embryonic development and survival of freshwater turtles. We provide insights about population trends of P. sinensis in the wild, and future directions for research.

How important is food structure when cats eat mice?

Feeding whole prey to felids has shown to benefit their gastrointestinal health. Whether this effect is caused by the chemical or physical nature of whole prey is unknown. Fifteen domestic cats, as a model for strict carnivores, were either fed minced mice (MM) or whole mice (WM), to determine the effect of food structure on digestibility, mean urinary excretion time (MUET) of 15N, intestinal microbial activity and fermentation products. Faeces samples were collected after feeding all cats a commercially available extruded diet (EXT) for 10 d before feeding for 19 d the MM and WM diets with faeces and urine collected from day 11 to 15. Samples for microbiota composition and determination of MUET were obtained from day 16 to 19. The physical structure of the mice diet (minced or not) did not affect large intestinal fermentation as total SCFA and branched-chain fatty acid (BCFA), and most biogenic amine (BA) concentrations were not different (P > 0·10). When changing from EXT to the mice diets, the microbial community composition shifted from a carbolytic (Prevotellaceae) to proteolytic (Fusobacteriaceae) profile and led to a reduced faecal acetic to propionic acid ratio, SCFA, total BCFA (P < 0·001), NH3 (P = 0·04), total BA (P < 0·001) and para-cresol (P = 0·08). The results of this study indicate that food structure within a whole-prey diet is less important than the overall diet type, with major shifts in microbiome and decrease in potentially harmful fermentation products when diet changes from extruded to mice. This urges for careful consideration of the consequences of prey-based diets for gut health in cats.

Prevalence of Fusobacterium Species in Endodontic Infections Detected With Molecular Methods: Systematic Review and Meta-Analysis

INTRODUCTION

Endodontic infections are polymicrobial; however, investigating the role of bacterial species is critical because they may influence pathogenesis, the development of symptoms, or the persistence of disease. This systematic review aimed to determine the prevalence of Fusobacterium species and its association with different types of endodontic infections.

METHODS

MEDLINE (Ovid), PubMed, Scopus, Web of Science, and Cochrane Library databases were used as electronic databases to retrieve relevant studies. The studies were evaluated for eligibility criteria, and the certainty in evidence and risk of bias were evaluated using critical appraisal tools for prevalence studies from the Joanna Briggs Institute. Forty studies were selected for meta-analysis and statistically analyzed for the relationship between the prevalence of Fusobacterium species and both the presence of symptoms and the type of infections (primary vs secondary/persistent) using meta-regression analysis.

RESULTS

The prevalence of Fusobacterium spp. in endodontic infections ranged from 3%-100% (mean = 42.51%) in the 40 included studies. Calculated confidence intervals indicated that the presence of Fusobacterium spp. was not statistically associated with the presence of symptoms or with the type of infections (the set of 2 predictors was not significant; P < .05).

CONCLUSIONS

The prevalence of Fusobacterium infection, which was identified with molecular methods, was not significant for overall regression using both predictors (ie, symptoms [symptomatic vs asymptomatic] and types of infections [primary vs secondary/persistent]).

The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats

BACKGROUND

Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.

RESULTS

The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats. In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.

CONCLUSIONS

This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.

Characteristics of Microbiota in Different Segments of the Digestive Tract of Lycodon rufozonatus

The gastrointestinal tract of animals contains microbiota, forming a complex microecosystem. Gut microbes and their metabolites can regulate the development of host innate and adaptive immune systems. Animal immune systems maintain intestinal symbiotic microbiota homeostasis. However, relatively few studies have been published on reptiles, particularly snakes, and even fewer studies on different parts of the digestive tracts of these animals. Herein, we used 16S rRNA gene sequencing to investigate the microbial community composition and adaptability in the stomach and small and large intestines of Lycodon rufozonatus. Proteobacteria, Bacteroidetes, and Firmicutes were most abundant in the stomach; Fusobacteria in the small intestine; and Proteobacteria, Bacteroidetes, Fusobacteria, and Firmicutes in the large intestine. No dominant genus could be identified in the stomach; however, dominant genera were evident in the small and large intestines. The microbial diversity index was significantly higher in the stomach than in the small and large intestines. Moreover, the influence of the microbial community structure on function was clarified through function prediction. Collectively, the gut microbes in the different segments of the digestive tract revealed the unique features of the L. rufozonatus gut microbiome. Our results provide insights into the co-evolutionary relationship between reptile gut microbiota and their hosts.

Are intratumoral microbiota involved in the progression of intraductal papillary mucinous neoplasms of the pancreas?

BACKGROUND

Microbiota have been reported to influence the development of various gastrointestinal neoplasms through the mechanism of sustained inflammation; however, few data are available regarding their influence on intraductal papillary mucinous neoplasms. The aim of this study was to assess the association between specific microbiota and the clinicopathologic characteristics of intraductal papillary mucinous neoplasms of the pancreas.

METHODS

DNA was extracted from formalin-fixed, paraffin-embedded samples of 30 patients who underwent pancreatectomy for intraductal papillary mucinous neoplasm, and polymerase chain reaction was used to create sequence libraries using the primer set for the V3 and V4 region of 16S recombinant DNA. Filtered sequence reads were then processed into operational taxonomic units with a 97% identity threshold and the relative abundance of bacteria compared between the 2 groups using operational taxonomic units.

RESULTS

There was a trend toward fewer Firmicutes and more Proteobacteria and Fusobacteria in the relative abundance of main duct operational taxonomic units than in branch duct operational taxonomic units. The relative abundances of Bacteroidetes (P < .01) and Fusobacteria (P = .04) were significantly higher in invasive intraductal papillary mucinous neoplasms than in noninvasive intraductal papillary mucinous neoplasms. The relative abundance of the intestinal type was significantly lower in Firmicutes than the relative abundance of the nonintestinal type (P = .04). Notably, main duct operational taxonomic units with the intestinal subtype were affected by increased proportions of Proteobacteria and Fusobacteria, and Fusobacteria were abundant in the intestinal type of invasive main duct operational taxonomic units.

CONCLUSION

Intratumoral microbiota may be involved in the progression of operational taxonomic units.

Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes

Fusobacterium necrophorum is a Gram-negative, filamentous anaerobe prevalent in the mucosal flora of animals and humans. It causes necrotic infections in cattle, resulting in a substantial economic impact on the cattle industry. Although infection severity and management differ within F. necrophorum species, little is known about F. necrophorum speciation and the genetic virulence determinants between strains. To characterize the clinical isolates, we performed whole-genome sequencing of four bovine isolates (8L1, 212, B17, and SM1216) and one human isolate (MK12). To determine the phylogenetic relationship and evolution pattern and investigate the presence of antimicrobial resistance genes (ARGs) and potential virulence genes of F. necrophorum, we also performed comparative genomics with publicly available Fusobacterium genomes. Using up-to-date bacterial core gene (UBCG) set analysis, we uncovered distinct Fusobacterium species and F. necrophorum subspecies clades. Pangenome analyses revealed a high level of diversity among Fusobacterium strains down to species levels. The output also identified 14 and 26 genes specific to F. necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme, respectively, which could be essential for bacterial survival under different environmental conditions. ClonalFrameML-based recombination analysis suggested that extensive recombination among accessory genes led to species divergence. Furthermore, the only strain of F. necrophorum with ARGs was F. necrophorum subsp. funduliforme B35, with acquired macrolide and tetracycline resistance genes. Our custom search revealed common virulence genes, including toxins, adhesion proteins, outer membrane proteins, cell envelope, type IV secretion system, ABC (ATP-binding cassette) transporters, and transporter proteins. A focused study on these genes could help identify major virulence genes and inform effective vaccination strategies against fusobacterial infections. IMPORTANCE Fusobacterium necrophorum is an anaerobic bacterium that causes liver abscesses in cattle with an annual incidence rate of 10% to 20%, resulting in a substantial economic impact on the cattle industry. The lack of definite biochemical tests makes it difficult to distinguish F. necrophorum subspecies phenotypically, where genomic characterization plays a significant role. However, due to the lack of a good reference genome for comparison, F. necrophorum subspecies-level identification represents a significant challenge. To overcome this challenge, we used comparative genomics to validate clinical test strains for subspecies-level identification. The findings of our study help predict specific clades of previously uncharacterized strains of F. necrophorum. Our study identifies both general and subspecies-specific virulence genes through a custom search-based analysis. The virulence genes identified in this study can be the focus of future studies aimed at evaluating their potential as vaccine targets to prevent fusobacterial infections in cattle.

The Role of the Human Gut Microbiome in Inflammatory Bowel Disease and Radiation Enteropathy

The human gut microbiome plays a key role in regulating host physiology. In a stable state, both the microbiota and the gut work synergistically. The overall homeostasis of the intestinal flora can be affected by multiple factors, including disease states and the treatments given for those diseases. In this review, we examine the relatively well-characterised abnormalities that develop in the microbiome in idiopathic inflammatory bowel disease, and compare and contrast them to those that are found in radiation enteropathy. We discuss how these changes may exert their effects at a molecular level, and the possible role of manipulating the microbiome through the use of a variety of therapies to reduce the severity of the underlying condition.

The relationship between dietary trophic level, parasites and the microbiome of Pacific walrus (Odobenus rosmarus divergens)

Arctic species are likely to experience rapid shifts in prey availability under climate change, which may alter their exposure to microbes and parasites. Here, we describe fecal bacterial and macroparasite communities and assess correlations with diet trophic level in Pacific walruses harvested during subsistence hunts by members of the Native Villages of Gambell and Savoonga on St Lawrence Island, Alaska. Fecal bacterial communities were dominated by relatively few taxa, mostly belonging to phyla Fusobacteriota and Firmicutes. Members of parasite-associated phyla Nematoda, Acanthocephala and Platyhelminthes were prevalent in our study population. We hypothesized that high versus low prey trophic level (e.g. fish versus bivalves) would result in different gut bacterial and macroparasite communities. We found that bacterial community structure correlated to diet, with nine clades enriched in walruses consuming higher-trophic-level prey. While no parasite compositional differences were found at the phylum level, the cestode genus Diphyllobothrium was more prevalent and abundant in walruses consuming higher-trophic-level prey, probably because fish are the intermediate hosts for this genus. This study suggests that diet is important for structuring both parasite and microbial communities of this culturally and ecologically important species, with potential implications for population health under climate change.

Gut microbiota analysis of Blenniidae fishes including an algae-eating fish and clear boundary formation among isolated Vibrio strains

Some marine fishes are algae-feeding, and the microorganisms in their digestive tracts produce carbohydrate hydrolyzing enzymes such as agarose and fucosidase, which are potentially interesting resource for new functional enzymes. The purpose of this study was to establish a method for identifying and utilizing characteristic bacteria from the intestines of two algae-eating fish species: Andamia tetradactylus, which exclusively eats algae on the rock surface, and stellar rockskipper Entomacrodus stellifer, which feeds on both algae and invertebrates. We tested the species composition of the intestinal bacterial flora and found that Proteobacteria were commonly found both in species as in the common gut communities of marine fish, whereas Spirochaetes and Tenericutes occupied the flora of A. tetradactylus. We then performed anaerobic and aerobic cultures and isolated 34 and 44 strains including 48 strains belonged to Vibrio species from A. tetradactylus and E. stellifer. We observed that some Vibrio strains formed a clear boundary to avoid contacting other strains of bacteria. Whole-genome sequencing of such two Vibrio alginolyticus strains revealed two cyclic chromosomes commonly found in the genome of Vibrio species, and some unique genes encoding alginate lyase, chitinases, and type I-F CRISPR-associated endoribonuclease for the first time in Vibrio alginolyticus.

Dysbiosis of skin microbiome and gut microbiome in melanoma progression

Background

The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy. Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. However, the role of the skin microbiome has not been well explored in the skin tumour microenvironment and the link between the gut microbiome and skin microbiome has not been investigated in melanoma progression. Therefore, the aim of the present study was to examine associations between dysbiosis in the skin and gut microbiome and the melanoma growth using MeLiM porcine model of melanoma progression and spontaneous regression.

Results

Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets. The bacterial composition of samples was analysed by high throughput sequencing of the V4-V5 region of the 16S rRNA gene. A significant difference in microbiome diversity and richness between melanoma tissue and healthy skin and between the faecal microbiome of MeLiM piglets and control piglets were observed. Both Principal Coordinate Analysis and Non-metric multidimensional scaling revealed dissimilarities between different bacterial communities. Linear discriminant analysis effect size at the genus level determined different potential biomarkers in multiple bacterial communities. Lactobacillus, Clostridium sensu stricto 1 and Corynebacterium 1 were the most discriminately higher genera in the healthy skin microbiome, while Fusobacterium, Trueperella, Staphylococcus, Streptococcus and Bacteroides were discriminately abundant in melanoma tissue microbiome. Bacteroides, Fusobacterium and Escherichia-Shigella were associated with the faecal microbiota of MeLiM piglets. Potential functional pathways analysis based on the KEGG database indicated significant differences in the predicted profile metabolisms between the healthy skin microbiome and melanoma tissue microbiome. The faecal microbiome of MeLiM piglets was enriched by genes related to membrane transports pathways allowing for the increase of intestinal permeability and alteration of the intestinal mucosal barrier.

Conclusion

The associations between melanoma progression and dysbiosis in the skin microbiome as well as dysbiosis in the gut microbiome were identified. Results provide promising information for further studies on the local skin and gut microbiome involvement in melanoma progression and may support the development of new therapeutic approaches.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02458-5.

Pathogenicity, infective dose and altered gut microbiota in piglets infected with porcine deltacoronavirus

Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus that cause severe diarrhea, resulting in high mortality in neonatal piglets. Little is known regarding the pathogenicity of PDCoV in different infective dose and the dynamic changes in the composition of the gut microbiota in PDCoV-induced diarrhea piglets. In this study, 5-day-old piglets were experimentally infected with different dose of PDCoV. The challenged piglets developed typical symptoms, characterized by acute and severe watery diarrhea from 1 to 8 days post-inoculation (DPI), and viral shedding was detected in rectal swab until 11 DPI. Tissues of small intestines displayed significant macroscopic and microscopic lesions with clear viral antigen expression. However, no significant differences among groups were found in challenged piglets. Then alteration in gut microbiota in the jejunum and colon of PDCoV infected-piglets were analyzed using 16S rRNA sequencing. PDCoV infection reduced bacterial diversity and richness, and significantly altered the structure and abundance of the microbiota from the phylum to genus. Fusobacterium, and Proteobacteria was significantly increased (P < 0.05), while the abundance of Bacteroidota was markedly decreased in the infected-piglets. Furthermore, microbial function prediction indicated that the changes in intestinal bacterial also affected the immune system, excretory system, circulatory system, neurodegenerative disease, cardiovascular disease, xenobiotics biodegradation and metabolism, etc. These findings suggest that regulating gut microbiota community may be an effective approach for preventing PDCoV infection.

The Effects of Ionizing Radiation on Gut Microbiota, a Systematic Review

BACKGROUND

The human gut microbiota is defined as the microorganisms that collectively inhabit the intestinal tract. Its composition is relatively stable; however, an imbalance can be precipitated by various factors and is known to be associated with various diseases. Humans are daily exposed to ionizing radiation from ambient and medical procedures, and gastrointestinal side effects are not rare.

METHODS

A systematic search of PubMed, EMBASE, and Cochrane Library databases was conducted. Primary outcomes were changes in composition, richness, and diversity of the gut microbiota after ionizing radiation exposure. Standard methodological procedures expected by Cochrane were used.

RESULTS

A total of 2929 nonduplicated records were identified, and based on the inclusion criteria, 11 studies were considered. Studies were heterogeneous, with differences in population and outcomes. Overall, we found evidence for an association between ionizing radiation exposure and dysbiosis: reduction in microbiota diversity and richness, increase in pathogenic bacteria abundance (Proteobacteria and Fusobacteria), and decrease in beneficial bacteria (Faecalibacterium and Bifidobacterium).

CONCLUSIONS

This review highlights the importance of considering the influence of ionizing radiation exposure on gut microbiota, especially when considering the side effects of abdominal and pelvic radiotherapy. Better knowledge of these effects, with larger population studies, is needed.

The impact of caries status on supragingival plaque and salivary microbiome in children with mixed dentition: a cross-sectional survey

Background

Supragingival plaque and saliva are commonly used for microbiome analysis. Many epidemiological studies have identified deciduous teeth caries as a risk factor for caries development in first permanent molar (FPM); nevertheless, to the best of our knowledge, there are no reports on the effects of deciduous teeth caries on the microbiome of healthy FPM. Additionally, it remains unclear whether saliva can be used instead of supragingival plaque for caries microbial studies. Therefore, we aimed to elucidate this issue, and to characterize and compare the oral microbiome of healthy FPMs in children with different caries statuses and that from children with and without caries in a similar microhabitat, by PacBio sequencing. Currently, few studies have investigated the oral microbiome of children using this technique.

Methods

Thirty children (aged 7–9 years) with mixed dentition were enrolled; 15 had dental caries, and 15 did not. Supragingival plaques of deciduous molars and maxillary FPMs, and non-stimulating saliva samples were collected. DNA was extracted and the v1–v9 regions of 16S rRNA were amplified. Subsequently, PacBio sequencing and bioinformatic analyses were performed for microbiome identification.

Results

The microbial alpha diversity of the saliva samples was lower than that of the supragingival plaque (p < 0.05); however, no differences were detected between deciduous teeth and FPMs (p > 0.05). In addition, the alpha and beta diversity of children with and without caries was also similar (p > 0.05). Nonmetric multidimensional scaling and Adonis analyses indicated that the microbial structure of salivary and supragingival plaque samples differ (p < 0.05). Further analysis of deciduous teeth plaque showed that Streptococcus mutans, Propionibacterium acidifaciens, and Veillonella dispar were more abundant in children with caries than in those without (p < 0.05); while in FPMs plaque, Selenomonas noxia was more abundant in healthy children (p < 0.05). No differences in microorganisms abundance were found in the saliva subgroups (p > 0.05).

Conclusion

We have determined that supragingival plaque was the best candidate for studying carious microbiome. Furthermore, S. mutans, V. dispar, and P. acidifaciens were highly associated with deciduous teeth caries. S. noxia may be associated with the abiding health of FPM; however, this requires additional studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-021-01683-0.

Isolated Septic Arthritis of the Hip Due to Fusobacterium Nucleatum in An Immunocompetent Adult: A Case Report and Review of the Literature

Introduction:

Hip septic arthritis is more common in children than in adults. Staphylococcus aureus and Streptococcus spp. are commonly found in association with septic joints. In contrast, Fusobacterium nucleatum septic arthritis in adults is extremely rare. To the best of our knowledge, only five cases have been reported in the literature in English, and three of them were cases of periprosthetic joint infection. We report a rare case of hip septic arthritis due to F. nucleatum in an immunocompetent adult.

Case Presentation:

A 56-year-old Asian man with a history of bilateral Perthes’ disease and mild alcoholic liver disease presented to our hospital complaining of worsening right hip pain and difficulty in walking for the previous 3 weeks. On presentation, his temperature was 38.7°C, and laboratory results showed a white blood cell count of 19 200 cells/µL and a C-reactive protein level of 43.56 mg/dL. Hip movements were limited due to pain. Contrast-enhanced computed tomography and magnetic resonance imaging showed fluid retention, suggesting infection. F. nucleatum was detected in the culture test from joint aspirate. Surgical drainage was performed 3 times in combination with antibiotherapy. Finally, we performed two-stage total hip arthroplasty, and the post-operative course was uneventful without implant loosening or infection relapse.

Conclusion:

The patient had a history of Perthes’ disease and had hip osteoarthritis, which may have contributed to the development of hip septic arthritis. We treated this rare case of hip septic arthritis due to F. nucleatum with two-stage revision surgery and antibiotherapy. Clinicians should be aware that F. nucleatum could be the etiologic agent of hip septic arthritis in an immunocompetent patient.

Sneathia: an emerging pathogen in female reproductive disease and adverse perinatal outcomes

Sneathia is an emerging pathogen implicated in adverse reproductive and perinatal outcomes. Although scarce, recent data suggest that vaginally residing Sneathia becomes pathogenic following its ascension into the upper urogenital tract, amniotic fluid, placenta, and foetal membranes. The role of Sneathia in women's health and disease is generally underappreciated because the cultivation of these bacteria is limited by their complex nutritional requirements, slow growth patterns, and anaerobic nature. For this reason, molecular methods are typically required for the detection and differential diagnosis of Sneathia infections. Here, we review the laboratory methods used for the diagnosis of Sneathia infections, the molecular mechanisms underlying its virulence, and its sensitivity to antibiotics. We further review the evidence of Sneathia's contributions to the pathogenesis of bacterial vaginosis, chorioamnionitis, preterm prelabour rupture of membranes, spontaneous preterm labour, stillbirth, maternal and neonatal sepsis, HIV infection, and cervical cancer. Collectively, growing evidence indicates that Sneathia represents an important yet underappreciated pathogen affecting the development and progression of several adverse clinical conditions diagnosed in pregnant women and their neonates, as well as in non-pregnant women.

Fusobacterium nucleatum Secretes Outer Membrane Vesicles and Promotes Intestinal Inflammation

Multiple studies have implicated microbes in the development of inflammation, but the mechanisms remain unknown. Bacteria in the genus Fusobacterium have been identified in the intestinal mucosa of patients with digestive diseases; thus, we hypothesized that Fusobacterium nucleatum promotes intestinal inflammation. The addition of >50 kDa F. nucleatum conditioned media, which contain outer membrane vesicles (OMVs), to colonic epithelial cells stimulated secretion of the proinflammatory cytokines interleukin-8 (IL-8) and tumor necrosis factor (TNF). In addition, purified F. nucleatum OMVs, but not compounds <50 kDa, stimulated IL-8 and TNF production; which was decreased by pharmacological inhibition of Toll-like receptor 4 (TLR4). These effects were linked to downstream effectors p-ERK, p-CREB, and NF-κB. F. nucleatum >50-kDa compounds also stimulated TNF secretion, p-ERK, p-CREB, and NF-κB activation in human colonoid monolayers. In mice harboring a human microbiota, pretreatment with antibiotics and a single oral gavage of F. nucleatum resulted in inflammation. Compared to mice receiving vehicle control, mice treated with F. nucleatum showed disruption of the colonic architecture, with increased immune cell infiltration and depleted mucus layers. Analysis of mucosal gene expression revealed increased levels of proinflammatory cytokines (KC, TNF, IL-6, IFN-γ, and MCP-1) at day 3 and day 5 in F. nucleatum-treated mice compared to controls. These proinflammatory effects were absent in mice who received F. nucleatum without pretreatment with antibiotics, suggesting that an intact microbiome is protective against F. nucleatum-mediated immune responses. These data provide evidence that F. nucleatum promotes proinflammatory signaling cascades in the context of a depleted intestinal microbiome.IMPORTANCE Several studies have identified an increased abundance of Fusobacterium in the intestinal tracts of patients with colon cancer, liver cirrhosis, primary sclerosing cholangitis, gastroesophageal reflux disease, HIV infection, and alcoholism. However, the direct mechanism(s) of action of Fusobacterium on pathophysiological within the gastrointestinal tract is unclear. These studies have identified that F. nucleatum subsp. polymorphum releases outer membrane vesicles which activate TLR4 and NF-κB to stimulate proinflammatory signals in vitro Using mice harboring a human microbiome, we demonstrate that F. nucleatum can promote inflammation, an effect which required antibiotic-mediated alterations in the gut microbiome. Collectively, these results suggest a mechanism by which F. nucleatum may contribute to intestinal inflammation.

Extreme storms cause rapid but short-lived shifts in nearshore subtropical bacterial communities

Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run-off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early- and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment - locally known as red soil pollution - and caused moderate increases of macronutrients, especially SiO₂ and PO₄ ^3-, with up to 25 and 0.5 μM respectively. We detected shifts in relative abundances of marine and terrestrially derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run-off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short-lived and bacterial communities quickly recovered following both storm events. The early- and late-season storms caused different physicochemical and bacterial community changes, demonstrating the context-dependency of extreme storm responses in a subtropical coastal ecosystem.

Rainbow darter (Etheostoma caeruleum) from a river impacted by municipal wastewater effluents have altered gut content microbiomes

Municipal wastewater treatment plant (WWTP) effluent contains pharmaceuticals and personal care products known to affect fish health and reproduction. The microbiome is a community of bacteria integral in maintaining host health and is influenced by species, diet, and environment. This study investigated changes in the diversity and composition of the gut content microbiome of rainbow darter (Etheostoma caeruleum) at ten sites on the Grand River, Ontario, Canada. Gut contents were collected in fall 2018 from these fish at sites upstream and downstream of two municipal wastewater treatment plants (WWTPs; Waterloo and Kitchener). 16S rRNA genes were sequenced to determine the composition and diversity (alpha and beta) of microbial taxa present. Gut content bacterial alpha diversity increased downstream of both WWTP outfalls; dominance of bacterial amplicon sequence variants decreased compared to upstream fish. Fish collected at different sites had distinct bacterial communities, with upstream samples dominant in Proteobacteria and Firmicutes, and downstream samples increasingly abundant in Proteobacteria and Cyanobacteria. In mammals, increased abundance of Proteobacteria is indicative of microbial dysbiosis and has been linked to altered health outcomes, but this is not yet known for fish. This research indicates that the fish gut content microbiome was altered downstream of WWTP effluent outfalls and could lead to negative health outcomes.

Effects of Thermal Stress on the Gut Microbiome of Juvenile Milkfish (Chanos chanos)

Milkfish, an important aquaculture species in Asian countries, are traditionally cultured in outdoor-based systems. There, they experience potentially stressful fluctuations in environmental conditions, such as temperature, eliciting changes in fish physiology. While the importance of the gut microbiome for the welfare and performance of fish has been recognized, little is known about the effects of thermal stress on the gut microbiome of milkfish and its interactions with the host’s metabolism. We investigated the gut microbiome of juvenile milkfish in a thermal stress experiment, comparing control (26 °C) and elevated temperature (33 °C) treatments over three weeks, analyzing physiological biomarkers, gut microbiome composition, and tank water microbial communities using 16S amplicon sequencing. The gut microbiome was distinct from the tank water and dominated by Cetobacterium, Enterovibrio, and Vibrio. We observed a parallel succession in both temperature treatments, with microbial communities at 33 °C differing more strongly from the control after the initial temperature increase and becoming more similar towards the end of the experiment. As proxy for the fish’s energy status, HSI (hepatosomatic index) was correlated with gut microbiome composition. Our study showed that thermal stress induced changes in the milkfish gut microbiome, which may contribute to the host’s habituation to elevated temperatures over time.

Full Femoral Osteomyelitis Caused by Fusobacterium nucleatum in an Immunocompetent Adult: A Case Report

CASE

We present a 46-year-old man who developed a full femoral osteomyelitis caused by Fusobacterium nucleatum. The subtle presentation of the infection and the late onset of appropriate antibiotic treatment caused a devastating bone quality of the full femur.

CONCLUSIONS

A successful outcome was obtained with surgical debridement, antibiotics, and return to weight bearing guided by a laboratory and radiographic scale specially designed to avoid pathologic fractures toward his full functional recovery.

Physiological parameters and gut microbiome associated with different dietary lipid levels in hybrid yellow catfish (Tachysurus fulvidraco♀× Pseudobagrus vachellii♂)

Yellow catfish are intensively farmed in China and are often fed a high-fat diet (HFD) with the aim of using less protein. However, an excess of dietary lipids is likely to affect the gut microflora, which strongly affects immunity and nutrient digestion. To determine the effects of different lipid levels on the growth, physiological parameters and gut microbiome of hybrid yellow catfish, we conducted an 8-week feeding experiment with a low-fat diet (2% lipids, LFD), a normal-fat diet (9% lipids, NFD), and a HFD (15% lipids) (120 fish per group). The HFD group showed higher serum alanine aminotransferase and aspartate transaminase activities, which suggests that excess dietary lipids cause liver damage. A total of 1138 operational taxonomic units, 11 phyla, and 117 genera were identified from fish gut samples. Neither the HFD nor the LFD strongly affected the microbial composition in gut samples. Compared with fish in the NFD, those in the HFD and LFD showed significantly decreased intestinal microbial diversity. The composition of macronutrients in the different diets affected the composition of intestinal microflora, mainly the phyla Fusobacteria, Proteobacteria, and Firmicutes. The HFD and the LFD favored the growth of Fusobacteria, while the HFD and LFD resulted in decreased abundance of Firmicutes and Proteobacteria, respectively. These findings shed light on the complex relationships among diet, intestinal microorganisms, and host metabolism. When using an HFD for farmed fish, its effects on the gut microbiome should be considered to avoid illness and poor growth.

Osmotic stress induces gut microbiota community shift in fish

Alteration of the gut microbiota plays an important role in animal health and metabolic diseases. However, little is known with respect to the influence of environmental osmolality on the gut microbial community. The aim of the current study was to determine whether the reduction in salinity affects the gut microbiota and identify its potential role in salinity acclimation. Using Oryzias melastigma as a model organism to perform progressive hypotonic transfer experiments, we evaluated three conditions: seawater control (SW), SW to 50% sea water transfer (SFW) and SW to SFW to freshwater transfer (FW). Our results showed that the SFW and FW transfer groups contained higher operational taxonomic unit microbiota diversities. The dominant bacteria in all conditions constituted the phylum Proteobacteria, with the majority in the SW and SFW transfer gut comprising Vibrio at the genus level, whereas this population was replaced by Pseudomonas in the FW transfer gut. Furthermore, our data revealed that the FW transfer gut microbiota exhibited a reduced renin-angiotensin system, which is important in SW acclimation. In addition, induced detoxification and immune mechanisms were found in the FW transfer gut microbiota. The shift of the bacteria community in different osmolality environments indicated possible roles of bacteria in facilitating host acclimation.

Characterization of the bacterial microbiome among free-ranging bottlenose dolphins (Tursiops truncatus)

Marine animals represent a dynamic and complex habitat for diverse microbial communities. The microbiota associated with bottlenose dolphins (Tursiops truncatus) are believed to influence their health status, but it remains poorly understood. We therefore characterized and compared the bacterial microbiome of bottlenose dolphins from six different anatomical sites that represent four different body systems (respiratory, digestive, reproductive, and integumentary). In this study, a total of 14 free-ranging bottlenose dolphins were sampled during the 2015 Sarasota Bay Dolphin Health Assessment. Bacterial diversity and abundance were assessed by PCR amplification of the hypervariable V3-V4 regions of the bacterial 16S rRNA gene for each sample, followed by sequencing on an Illumina MiSeq platform. Analysis showed that bottlenose dolphins harbor diverse bacterial communities with a unique microbial community at each body system. Additionally, the bottlenose dolphin bacterial microbiome was clearly distinct to the aquatic microbiome from their surrounding habitat. These results are in close agreement with other cetacean microbiome studies, while our study is the first to explore what was found to be a diverse bottlenose dolphin genital microbiome. The core bacterial communities identified in this study in apparently healthy animals might be informative for future health monitoring of bottlenose dolphins.

Dendrobium officinale Kimura et Migo and American ginseng mixture: A Chinese herbal formulation for gut microbiota modulation

Dendrobium officinale Kimura et Migo (D. officinale) is a famous traditional Chinese medicine (TCM). A mixture of D. officinale and American ginseng has been shown to enhance cell-mediated immunity, humoral immunity, and monocyte/macrophage functions in mice. Here, the effects of a D. officinale and American ginseng mixture on the structure of gut microbial community in dogs were examined using high-throughput 16S rRNA gene amplicon sequencing. The data revealed that while the mixture did not change the diversity of gut microbial community significantly, differences among individuals were significantly reduced. Furthermore, the mixture-responsive operational taxonomic units (OTUs) exhibited a phase-dependent expression pattern. Fifty-five OTUs were found to exhibit a mixture-induced expression pattern, among which one third were short-chain fatty acid (SCFA)-producing genera and the others were probiotic genera included Lactobacillus spp., Sutterella, Alistipes, Anaerovorax, Bilophila, Coprococcus, Gordonibacter, Oscillibacter, among others. By contrast, 36% of the OTUs exhibiting a mixture-repressed expression pattern were disease-associated microorganisms, and six genera, namely Actinomyces, Escherichia/Shigella, Fusobacterium, Slackia, Streptococcus and Solobacterium, were associated with cancer. In addition, five genera were closely associated with diabetes, namely Collinsella, Rothia, Howardella, Slackia and Intestinibacter. Our results indicate that this D. officinale and American ginseng mixture may be used as a prebiotic agent to enhance SCFA-producing genera and prevent gut dysbiosis.

Insights into the Natural Defenses of a Coral Reef Fish Against Gill Ectoparasites: Integrated Metabolome and Microbiome Approach

Understanding natural defense mechanisms against parasites can be a valuable tool for the development of innovative therapies. We have previously identified a butterflyfish species (Chaetodon lunulatus) that avoids gill monogenean parasites while living amongst closely related parasitized species. The metabolome and microbiome of several sympatric butterflyfish species from the island of Moorea (French Polynesia) were previously described. In this study, we used the previously generated datasets in an attempt to identify metabolites and bacteria potentially involved in parasite defense mechanisms. We investigated the interplay between the gill mucus metabolome and microbiome of the non-susceptible C. lunulatus versus sympatric butterflyfish species that were always found parasitized in the Central and Eastern Indo-Pacific. After observing significant differences between the metabolome and bacteria of susceptible versus non-susceptible fish, we obtained the discriminant metabolites and operational taxonomic units (OTUs) using a supervised analysis. Some of the most important discriminant metabolites were identified as peptides, and three new peptides derived from β-subunit hemoglobin from C. lunulatus (CLHbβ-1, CLHbβ-2, and CLHbβ-3) were purified, characterized and synthesized to confirm their structures. We also identified specific bacterial families and OTUs typical from low-oxygen habitats in C. lunulatus gill mucus. By using a correlation network between the two datasets, we found a Fusobacteriaceae strain exclusively present in C. lunulatus and highly correlated to the peptides. Finally, we discuss the possible involvement of these peptides and Fusobacteriaceae in monogenean avoidance by this fish species.

After the bite: bacterial transmission from grey seals (Halichoerus grypus) to harbour porpoises (Phocoena phocoena)

Recent population growth of the harbour porpoise (Phocoena phocoena), grey seal (Halichoerus grypus) and common seal (Phoca vitulina) in the North Sea has increased potential interaction between these species. Grey seals are known to attack harbour porpoises. Some harbour porpoises survive initially, but succumb eventually, often showing severely infected skin lesions. Bacteria transferred from the grey seal oral cavity may be involved in these infections and eventual death of the animal. In humans, seal bites are known to cause severe infections. In this study, a 16S rRNA-based microbiome sequencing approach is used to identify the oral bacterial diversity in harbour porpoises, grey seals and common seals; detect the potential transfer of bacteria from grey seals to harbour porpoises by biting and provide insights in the bacteria with zoonotic potential present in the seal oral cavity. β-diversity analysis showed that 12.9% (4/31) of the harbour porpoise skin lesion microbiomes resembled seal oral microbiomes, while most of the other skin lesion microbiomes also showed seal-associated bacterial species, including potential pathogens. In conclusion, this study shows that bacterial transmission from grey seals to harbour porpoises by biting is highly likely and that seal oral cavities harbour many bacterial pathogens with zoonotic potential.

A comparison of nonlethal sampling methods for amphibian gut microbiome analyses

Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.

Advances in the mechanism of high copper diets in restraining pigs growth

High copper feed has been widely used as an inexpensive and highly effective feed additive to promote growth performance of pigs. However, long-term feeding of high copper feed may reduce the growth-promoting effects of copper, time-dependent accumulation of copper in animal tissues and organs, and copper toxicity thereby reducing the growth performance of pigs. Due to the widespread effects of high copper supplementation in animals' diets, the benefits and drawbacks of high copper feeding in pigs have been reported in several studies. Meanwhile, few of these studies have systematically described the mechanism by which high copper diets restrain pig growth. Therefore, to address the concerns and give a better understanding of the mechanism of high copper diet in restraining pig growth in different systems, this paper reviews the research progress of long-term supplementation of high copper on the growth of pigs and provides some suggestions and further research directions.

Enhanced Microbial Interactions and Deterministic Successions During Anoxic Decomposition of Microcystis Biomass in Lake Sediment

Microcystis biomass remineralization after blooming represents a hotspot of nutrient recycling in eutrophic lakes. Because Microcystis blooms are massively deposited on lake sediments, resulting in anoxic conditions, it is important to understand the response and role of benthic microbial communities during the anoxic decomposition of Microcystis in freshwater lakes. In the present study, we employed a microcosm method, combined with high-throughput sequencing, functional prediction, and network analysis, to investigate microbial succession during the short-term (30 days) anaerobic decomposition of Microcystis in a eutrophic sediment. Continuous accumulation of CH4 and CO2 and increasing relative abundance of methanogens were observed during the incubation. The microbial community composition (MCC) significantly changed after addition of Microcystis biomass, with a shift in the community from a stochastic to a functional, deterministic succession. Families, including Clostridiaceae, Rhodocyclaceae, Rikenellaceae, Peptostreptococcaceae, Syntrophomonadaceae, Lachnospiraceae, and Methanosarcinaceae, were predominantly enriched and formed diverse substitution patterns, suggesting a synergistic action of these family members in the decomposition of Microcystis biomass. Importantly, intense species-to-species interactions and weak resistance to disturbance were observed in the microbial community after Microcystis biomass addition. Collectively, these results suggest that the addition of Microcystis induce phylogenetic clustering and structure instability in the sediment microbial community and the synergistic interactions among saprotrophic bacteria play a key role in Microcystis biomass remineralization.

Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada

Rhizosphere and root associated bacteria are key components of plant microbiomes and influence crop production. In sustainable agriculture, it is important to investigate bacteria diversity in various plant species and how edaphic factors influence the bacterial microbiome. In this study, we used high-throughput sequencing to assess bacterial communities associated with the rhizosphere and root interior of canola, wheat, field pea, and lentil grown at four locations in Saskatchewan, Canada. Rhizosphere bacteria communities exhibited distinct profiles among crops and sampling locations. However, each crop was associated with distinct root endophytic bacterial communities, suggesting that crop species may influence the selection of root bacterial microbiome. Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in the root interior, whereas Gemmatimonadetes, Firmicutes, and Acidobacteria were prevalent in the rhizosphere soil. Pseudomonas and Stenotrophomonas were predominant in the rhizosphere and root interior, whereas Acinetobacter, Arthrobacter, Rhizobium, Streptomyces, Variovorax, and Xanthomonas were dominant in the root interior of all crops. The relative abundance of specific bacterial groups in the rhizosphere correlated with soil pH and silt and organic matter contents; however, there was no correlation between root endophytes and analyzed soil properties. These results suggest that the root microbiome may be modulated by plant factors rather than soil characteristics.

Concurrent fusobacterial pyogenic liver abscess and empyema

We present a very rare case of concurrent empyema and liver abscess caused by Fusobacterium. Our patient presented with 3-month history of subtle abdominal discomfort and cough leading to eventually presenting with marked chest pain, dyspnoea and septic shock. CT revealed a liver abscess and large right-sided pleural effusion. Drainage of the pleural effusion yielded gross pus with the growth of Fusobacterium varium, while drainage of the liver abscess yielded Fusobacterium nucleatum The patient responded to drainage and antibiotic therapy with resolution of symptoms and decrease in the size of empyema and abscess on follow-up imaging. We also include a review if literature of related fusobacterial infections.

Characteristics of biological particulate matters at urban and rural sites in the North China Plain

Depending on their concentrations, sizes, and types, particulate matters of biological origins (bioPM) significantly affect human health. However, for different air environments, they are not well characterized and can vary considerably. As an example, we investigated the bioPM differences at an urban (Beijing) site and a rural (Wangdu) site in the North China Plain (NCP) using an online monitoring instrument, an ultraviolet aerodynamic particle sizer (UV-APS), the limulus amebocyte lysate (LAL) assay, and a high-throughput sequencing method. Generally, lower concentrations of viable bioPM (hourly mean: 1.3 × 10³ ± 1.6 × 10³ m^-3) and endotoxin (0.66 ± 0.16 EU/m³) in Beijing were observed compared to viable bioPM (0.79 × 10⁵ ± 1.4 × 10⁵ m^-3) and endotoxin (15.1 ± 23.96 EU/m³) at the Wangdu site. The percentage of viable bioPM number concentration in the total PM was 3.1% in Beijing and 6.4% in Wangdu. Approximately 80% of viable bioPM was found to be in the range from 1 to 2.5 μm. Nevertheless, the size distribution patterns for viable bioPM at the Beijing and Wangdu sites differed and were affected by PM pollution, leading to distinct lung deposition profiles. Moreover, the distinct diurnal variations in viable bioPM on clean days were dimmed by the PM pollution at both sites. Distinct bacterial community structures were found in the air from the Beijing and Wangdu sites. The bacterial community in urban Beijing was dominated by genus Lactococcus (49.5%) and Pseudomonas (15.1%), while the rural Wangdu site was dominated by Enterococcus (65%) and Paenibacillus (10%). Human-derived genera, including Myroides, Streptococcus, Propionibacterium, Dietzia, Helcococcus, and Facklamia, were higher in Beijing, suggesting bacterial emission from humans in the urban air environment. Our results show that different air harbors different biological species, and people residing in different environments thus could have very different biological particle exposure.

Microbial Dynamics of Biosand Filters and Contributions of the Microbial Food Web to Effective Treatment of Wastewater-Impacted Water Sources

Biosand filtration systems are widely used for drinking water treatment, from household-level, intermittently operated filters to large-scale continuous municipal systems. While it is well-established that microbial activity within the filter is essential for the removal of potential pathogens and other contaminants, the microbial ecology of these systems and how microbial succession relates to their performance remain poorly resolved. We determined how different source waters influence the composition, temporal dynamics, and performance of microbial communities in intermittently operated biosand filters. We operated lab-scale biosand filters, adding daily inputs from two contrasting water sources with differing nutrient concentrations and found that total coliform removal increased and became less variable after 4 weeks, regardless of water source. Total effluent biomass was also lower than total influent biomass for both water sources. Bacterial community composition, assessed via cultivation-independent DNA sequencing, varied by water source, sample type (influent, effluent, or sand), and time. Despite these differences, we identified specific taxa that were consistently removed, including common aquatic and wastewater bacteria. In contrast, taxa consistently more abundant in the sand and effluent included predatory, intracellular, and symbiotic bacteria.IMPORTANCE Although microbial activities are known to contribute to the effectiveness of biosand filtration for drinking water treatment, we have a limited understanding of what microbial groups are most effectively removed, colonize the sand, or make it through the filter. This study tracked the microbial communities in the influent, sand, and effluent of lab-scale, intermittently operated biosand filters over 8 weeks. These results represent the most detailed and time-resolved investigation of the microbial communities in biosand filters typical of those implemented at the household level in many developing countries. We show the importance of the microbial food web in biosand filtration, and we identified taxa that are preferentially removed from wastewater-impacted water sources. We found consistent patterns in filter effectiveness from source waters with differing nutrient loads and, likewise, identified specific bacterial taxa that were consistently more abundant in effluent waters, taxa that are important targets for further study and posttreatment.

Use of Direct Hemoperfusion with Polymyxin B-Immobilized Fiber for the Treatment of Septic Shock Complicated with Lemierre Syndrome Caused by Fusobacterium necrophorum

We report a case of septic shock treated with PMX-DHP that was complicated with Lemierre syndrome caused by Fusobacterium necrophorum. The patient was a 31-year-old man who was initially diagnosed with influenza. He received treatment; however, because his symptoms gradually worsened, he was transported to our hospital 10 days following his diagnosis. His initial examination revealed symptoms of respiratory distress and an altered level of consciousness. Based on laboratory and imaging results, it became clear that he suffered from septic shock of unknown etiology, disseminated intravascular coagulation, and acute renal and respiratory failure. We initiated treatment with vasopressors, an antibacterial agent, immunoglobulins as well as an appropriate ventilator management; however, his unstable circulatory condition continued. As soon as PMX-DHP was initiated, 2 days following admission to the ICU, his circulatory instability normalized. F. necrophorum was ultimately detected after a culture examination, and contrast-enhanced computed tomography revealed a jugular vein thrombus, which led to the diagnosis of Lemierre syndrome. The patient's condition gradually improved, and he was discharged from the ICU after 19 days.

Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary

Marine biogeographic boundaries act as barriers to dispersal for many animal species, thereby creating distinctive faunas on either side. However, how such boundaries affect the distributions of microbial taxa remains poorly known. To test whether biogeographic boundaries influence the diversity and composition of host-associated microbiota, we analysed the microbiomes of three species of common intertidal gastropods at two sites separated by the biogeographic boundary at Point Conception (PtC), CA, using 16S rRNA gene sequencing. Our results show that each host species shows microbiome compositional specificity, even across PtC, and that alpha diversity does not change significantly across this boundary for any of the gastropod hosts. However, for two of the host species, beta diversity differs significantly across PtC, indicating that there may be multiple levels of organization of the marine gastropod microbiome. Overall, our results suggest that while biogeographic boundaries do not constrain the distribution of a core set of microbes associated with each host species, they can play a role in structuring the transient portion of the microbiome.

The Composition, Diversity and Predictive Metabolic Profiles of Bacteria Associated With the Gut Digesta of Five Sea Urchins in Luhuitou Fringing Reef (Northern South China Sea)

Sea urchins strongly affect reef ecology, and the bacteria associated with their gut digesta have not been well studied in coral reefs. In the current study, we analyze the bacterial composition of five sea urchin species collected from Luhuitou fringing reef, namely Stomopneustes variolaris, Diadema setosum, Echinothrix calamaris, Diadema savignyi, and Tripneustes gratilla, using high-throughput 16S rRNA gene-based pyrosequencing. Propionigenium, Prolixibacter, and Photobacterium were found to be the dominant bacterial genera in all five species. Interestingly, four sea urchin species, including S. variolaris, D. setosum, E. calamaris, and D. savignyi, displayed a higher mean total abundance of the three bacterial genera (69.72 ± 6.49%) than T. gratilla (43.37 ± 13.47%). Diversity analysis indicated that the gut digesta of sea urchin T. gratilla displayed a higher bacterial α-diversity compared with the other four species. PCoA showed that the four groups representing D. setosum, D. savignyi, E. calamaris, and S. variolaris were overlapping, but distant from the group representing T. gratilla. Predictive metagenomics performed by PICRUSt revealed that the abundances of genes involved in amino acid metabolism and metabolism of terpenoid and polyketide were higher in T. gratilla, while those involved in carbohydrate metabolism were higher in the other four sea urchin species. Therefore, our results indicated that the composition, diversity and predictive metabolic profiles of bacteria associated with the gut digesta of T. gratilla were significantly different from those of the other four sea urchin species in Luhuitou fringing reef.

Characterizing the microbiota in gastrointestinal tract segments of Rhabdophis subminiatus: Dynamic changes and functional predictions

The gut microbiota helps the host to absorb nutrients and generate immune responses that can affect host behavior, development, reproduction, and overall health. However, in most of the previous studies, microbiota was sampled mainly using feces and intestinal contents from mammals but not from wild reptiles. Here, we described the bacterial profile from five different gastrointestinal tract (GIT) segments (esophagus, stomach, small intestine, large intestine, and cloaca) of three wild Rhabdophis subminiatus using 16S rRNA V4 hypervariable amplicon sequencing. Forty-seven bacterial phyla were found in the entire GIT, of which Proteobacteria, Firmicutes, and Bacteroidetes were predominant. The results showed a significant difference in microbial diversity between the upper GIT segments (esophagus and stomach) and lower GIT segments (large intestine and cloaca). An obvious dynamic distribution of Fusobacteria and Bacteroidetes was observed, which mainly existed in the lower GIT segments. Conversely, the distribution of Tenericutes was mainly observed in the upper GIT. We also predicted the microbial functions in the different GIT segments, which showed that microbiota in each segments played an important role in higher membrane transport and carbohydrate and amino acid metabolism. Microbes in the small intestine were also mainly involved in disease-related systems, while in the large intestine, they were associated with membrane transport and carbohydrate metabolism. This is the first study to investigate the distribution of the gut microbiota and to predict the microbial function in R. subminiatus. The composition of the gut microbiota certainly reflects the diet and the living environment of the host. Furthermore, these findings provide vital evidence for the diagnosis and treatment of gut diseases in snakes and offer a direction for a model of energy budget research.

Degradation of antibiotics and antibiotic resistance genes in fermentation residues by ionizing radiation: A new insight into a sustainable management of antibiotic fermentative residuals

Antibiotic fermentative residues are categorized into hazardous wastes in China due to the existence of antibiotic resistance genes (ARGs) and residual antibiotics How to treat and manage these wastes is a new challenge. This paper investigated the treatment of erythromycin thiocyanate fermentation (EryTcF) residues using ionizing radiation technology for removing ARGs and antibiotics from the fermentation residues. The results showed that as exposed the EryTcF residues to gamma radiation, the abundance of four macrolide resistance genes (ereA, ermB, mefA and mpfB) decreased 1.0-1.3 log with 90-95% removal, and around 56% of erythromycin was removed at absorbed dose of 30&#x202F;kGy and room temperature (19-22&#x202F;°C). Direct action of γ-ray radiation contributed to 42-53% of ARGs removal and indirect action (radicals' reaction) was mainly responsible for erythromycin removal (84%). The positive correlation between total ARGs and Shannon index was observed. The potential ARGs-linked hosts were assigned to genera Aeromonas and Enterobacteriaceae and their abundance decreased by 36-43% at 30&#x202F;kGy. Radiation has not obvious influence on the nutrient components of residues, such as protein content, suggesting that the radiation treated fermentative residues can be used as fertilizer, which is favorable for the development of recycling economy in antibiotic pharmaceutical factory. The results could provide a new insight into a sustainable management of antibiotic fermentative residuals.

Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers

Proteins from the ferredoxin (Fd) and flavodoxin (Fld) families function as low potential electrical transfer hubs in cells, at times mediating electron transfer between overlapping sets of oxidoreductases. To better understand protein electron carrier (PEC) use across the domains of life, we evaluated the distribution of genes encoding [4Fe-4S] Fd, [2Fe-2S] Fd, and Fld electron carriers in over 7,000 organisms. Our analysis targeted genes encoding small PEC genes encoding proteins having ≤200 residues. We find that the average number of small PEC genes per Archaea (~13), Bacteria (~8), and Eukarya (~3) genome varies, with some organisms containing as many as 54 total PEC genes. Organisms fall into three groups, including those lacking genes encoding low potential PECs (3%), specialists with a single PEC gene type (20%), and generalists that utilize multiple PEC types (77%). Mapping PEC gene usage onto an evolutionary tree highlights the prevalence of [4Fe-4S] Fds in ancient organisms that are deeply rooted, the expansion of [2Fe-2S] Fds with the advent of photosynthesis and a concomitant decrease in [4Fe-4S] Fds, and the expansion of Flds in organisms that inhabit low-iron host environments. Surprisingly, [4Fe-4S] Fds present a similar abundance in aerobes as [2Fe-2S] Fds. This bioinformatic study highlights understudied PECs whose structure, stability, and partner specificity should be further characterized.

Etiologic role of root canal infection in apical periodontitis and its relationship with clinical symptomatology

Evidence shows the polymicrobial etiology of endodontic infections, in which bacteria and their products are the main agents for the development, progression, and dissemination of apical periodontitis. Microbial factors in necrotic root canals (e.g., endotoxin) may spread into apical tissue, evoking and supporting a chronic inflammatory load. Thus, apical periodontitis is the result of the complex interplay between microbial factors and host defense against invasion of periradicular tissues. This review of the literature aims to discuss the complex network between endodontic infectious content and host immune response in apical periodontitis. A better understanding of the relationship of microbial factors with clinical symptomatology is important to establish appropriate therapeutic procedures for a more predictable outcome of endodontic treatment.

Microbial community and functions associated with digestion of algal polysaccharides in the visceral tract of Haliotis discus hannai: Insights from metagenome and metatranscriptome analysis

Haliotis discus hannai, a species of Pacific abalone, is a highly valuable food source throughout Northeast Asia. As H. discus hannai primarily feed on brown algae and largely extract their energy from algal polysaccharides, understanding the mechanisms by which they digest algal polysaccharides is essential for elucidating their energy metabolism. Gut microbes, as well as the host animal, are involved in the process of polysaccharide degradation. To identify algal polysaccharide-digestion mechanisms and their origin, we analyzed the metagenome and metatranscriptome of abalone visceral extracts. Microbial communities were characterized using the 16S rRNA gene sequences in the metagenome and our results differed significantly from those of previous studies using traditional microbiological methods such as bacterial cultivation and cloning. A greater diversity of bacterial taxa was identified here than was previously identified using cultivation methods. Furthermore, the most abundant bacterial taxa also differed from previous studies, which is not common when comparing the results of bacterial culturing with those of molecular methodologies. Based on the metatranscriptome, overall functions were identified and additional analyses were performed on the coding sequences of algal polysaccharide-digestive enzymes, including alginate lyase. Results of the transcriptomic analyses suggest that alginate lyase in the visceral extracts of H. discus hannai was produced by the host itself, not by visceral bacteria. This is the first next-generation sequencing study performed on abalone to characterize the visceral microbiota and the source of the ability to digest algal polysaccharides by analyzing the metagenome and metatranscriptome together.

Multi-targeting therapeutic mechanisms of the Chinese herbal medicine QHD in the treatment of non-alcoholic fatty liver disease

Beneficial effects of the Chinese herbal medicine Qushi Huayu Decoction (QHD) were observed with non-alcoholic fatty liver disease (NAFLD) patients and animal models. The impact of QHD or its active components (geniposide and chlorogenic acid, GC) on NAFLD liver transcriptome and gut microbiota was examined with NAFLD rats. Increased expression for genes required for glutathione production and decreased expression for genes required for lipid synthesis was observed in NAFLD livers treated with QHD and GC. GC treatment decreased serum LPS, which could be explained by reduced mucosal damage in the colon of GC-treated rats. Further, our data suggest an increased abundance of Treg-inducing bacteria that stimulated the Treg activity in GC treated colon, which in turn down-regulated inflammatory signals, improved gut barrier function and consequently reduced hepatic exposure to microbial products. Our study suggests that QHD simultaneously enhanced the hepatic anti-oxidative mechanism, decreased hepatic lipid synthesis, and promoted the regulatory T cell inducing microbiota in the gut.

Effects of predation stress and food ration on perch gut microbiota

BACKGROUND

Gut microbiota provide functions of importance to influence hosts' food digestion, metabolism, and protection against pathogens. Factors that affect the composition and functions of gut microbial communities are well studied in humans and other animals; however, we have limited knowledge of how natural food web factors such as stress from predators and food resource rations could affect hosts' gut microbiota and how it interacts with host sex. In this study, we designed a two-factorial experiment exposing perch (Perca fluviatilis) to a predator (pike, Esox lucius), and different food ratios, to examine the compositional and functional changes of perch gut microbiota based on 16S rRNA amplicon sequencing. We also investigated if those changes are host sex dependent.

RESULTS

We showed that overall gut microbiota composition among individual perch significantly responded to food ration and predator presence. We found that species richness decreased with predator presence, and we identified 23 taxa from a diverse set of phyla that were over-represented when a predator was present. For example, Fusobacteria increased both at the lowest food ration and at predation stress conditions, suggesting that Fusobacteria are favored by stressful situations for the host. In concordance, both food ration and predation stress seemed to influence the metabolic repertoire of the gut microbiota, such as biosynthesis of other secondary metabolites, metabolism of cofactors, and vitamins. In addition, the identified interaction between food ration and sex emphasizes sex-specific responses to diet quantity in gut microbiota.

CONCLUSIONS

Collectively, our findings emphasize an alternative state in gut microbiota with responses to changes in natural food webs depending on host sex. The obtained knowledge from this study provided us with an important perspective on gut microbiota in a food web context.