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Intestinal gluconeogenesis (IGN), gastric bypass (GBP) and gut microbiota positively regulate glucose homeostasis and diet-induced dysmetabolism. GBP modulates gut microbiota, whether IGN could shape it has not been investigated. We studied gut microbiota and microbiome in wild type and IGN-deficient mice, undergoing GBP or not, and fed on either a normal chow (NC) or a high-fat/high-sucrose (HFHS) diet. We also studied fecal and urine metabolome in NC-fed mice. IGN and GBP had a different effect on the gut microbiota of mice fed with NC and HFHS diet. IGN inactivation increased abundance of Deltaproteobacteria on NC and of Proteobacteria such as Helicobacter on HFHS diet. GBP increased abundance of Firmicutes and Proteobacteria on NC-fed WT mice and of Firmicutes, Bacteroidetes and Proteobacteria on HFHS-fed WT mice. The combined effect of IGN inactivation and GBP increased abundance of Actinobacteria on NC and the abundance of Enterococcaceae and Enterobacteriaceae on HFHS diet. A reduction was observed in the amounf of short-chain fatty acids in fecal (by GBP) and in both fecal and urine (by IGN inactivation) metabolome. IGN and GBP, separately or combined, shape gut microbiota and microbiome on NC- and HFHS-fed mice, and modify fecal and urine metabolome., (© 2022. The Author(s).)

The gut microbiome (GMB), comprising the commensal microbial communities located in the gastrointestinal tract, has co-evolved in mammals to perform countless micro-ecosystem services to facilitate physiological functions. Because of the complex inter-relationship between mammals and their gut microbes, the number of studies addressing the role of the GMB on mammalian health is almost exclusively limited to human studies and model organisms. Furthermore, much of our knowledge of wildlife-GMB relationships is based on studies of colonic GMB communities derived from the feces of captive specimens, leaving our understanding of the GMB in wildlife limited. To better understand wildlife-GMB relationships, we engaged hunters as citizen scientists to collect biological samples from legally harvested black bears (Ursus americanus) and used 16S rRNA gene amplicon sequencing to characterize wild black bear GMB communities in the colon and jejunum, two functionally distinct regions of the gastrointestinal tract. We determined that the jejunum and colon of black bears do not harbor significantly different GMB communities: both gastrointestinal sites were dominated by Firmicutes and Proteobacteria. However, a number of bacteria were differentially enriched in each site, with the colon harboring twice as many enriched taxa, primarily from closely related lineages.

The white leg Litopenaeus vannamei shrimp is of importance to the eastern Pacific fisheries and aquaculture industry but suffer from diseases such as the recently emerged early mortality syndrome. Many bacterial pathogens have been identified but the L. vannamei microbiota is still poorly known. Using a next-generation sequencing (NGS) approach, this work evaluated the impact of the inclusion in the diet of mannan oligosaccharide, (MOS, 0.5% w/w), over the L. vannamei microbiota and production behavior of L. vannamei under intensive cultivation in Ecuador. The MOS supplementation lasted for 60 days, after which the shrimp in the ponds were harvested, and the production data were collected. MOS improved productivity outcomes by increasing shrimp survival by 30%. NGS revealed quantitative differences in the shrimp microbiota between MOS and control conditions. In the treatment with inclusion of dietary MOS, the predominant phylum was Actinobacteria (28%); while the control group was dominated by the phylum Proteobacteria (30%). MOS has also been linked to an increased prevalence of Lactococcus- and Verrucomicrobiaceae-like bacteria. Furthermore, under the treatment of MOS, the prevalence of potential opportunistic pathogens, like Vibrio, Aeromonas, Bergeyella and Shewanella, was negligible. This may be attributable to MOS blocking the adhesion of pathogens to the surfaces of the host tissues. Together, these findings point to the fact that the performance (survival) improvements of the dietary MOS may be linked to the impact on the microbiota, since bacterial lines with pathogenic potential towards shrimps were excluded in the gut.

The composition of fungal and bacterial communities in three polythermal glaciers and associated aquatic environments in Kongsfjorden, Svalbard was analysed using a combination of cultivation and amplicon sequencing. 109 fungal strains belonging to 30 mostly basidiomycetous species were isolated from glacial samples with counts up to 10 3 CFU/100 ml. Glaciozyma-related taxon and Phenoliferia psychrophenolica were the dominant species. Unexpectedly, amplicon sequencing uncovered sequences of Chytridiomycota in all samples and Rozellomycota in sea water, lake water, and tap water. Sequences of Malassezia restricta and of the extremely halotolerant Hortaea werneckii were also found in subglacial habitats for the first time. Overall, the fungal communities within a glacier and among glaciers were diverse and spatially heterogenous. Contrary to this, there was a large overlap between the bacterial communities of different glaciers, with Flavobacterium sp. being the most frequently isolated. In amplicon sequencing Actinobacteria and Proteobacteria sequences were the most abundant.

Interrelations between epiphytic bacteria and macroalgae are multifaceted and complicated, though little is known about the community structure, interaction and functions of those epiphytic bacteria. This study comprehensively characterized the epiphytic bacterial communities associated with eight different common seaweeds collected from a rocky intertidal zone on the Indian Ocean at Cape Vidal, South Africa. High-throughput sequencing analyses indicated that seaweed-associated bacterial communities were dominated by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Energy-dispersive X-ray (EDX) analysis showed the presence of elemental composition in the surface of examined seaweeds, in varying concentrations. Cluster analysis showed that bacterial communities of brown seaweeds (SW2 and SW4) were closely resembled those of green seaweeds (SW1) and red seaweeds (SW7) while those of brown seaweeds formed a separate branch. Predicted functional capabilities of epiphytic bacteria using PICRUSt analysis revealed abundance of genes related to metabolic and biosynthetic activities. Further important identified functional interactions included genes for bacterial chemotaxis, which could be responsible for the observed association and network of elemental-microbes interaction. The study concludes that the diversity of epiphytic bacteria on seaweed surfaces is greatly influenced by algal organic exudates as well as elemental deposits on their surfaces, which triggers chemotaxis responses from epiphytic bacteria with the requisite genes to metabolise those substrates.

The productivity of ruminants depends largely on rumen microbiota. However, there are few studies on the age-related succession of rumen microbial communities in grazing lambs. Here, we conducted 16 s rRNA gene sequencing for bacterial identification on rumen fluid samples from 27 Tibetan lambs at nine developmental stages (days (D) 0, 2, 7, 14, 28, 42, 56, 70, and 360, n = 3). We observed that Bacteroidetes and Proteobacteria populations were significantly changed during the growing lambs' first year of life. Bacteroidetes abundance increased from 18.9% on D0 to 53.9% on D360. On the other hand, Proteobacteria abundance decreased significantly from 40.8% on D0 to 5.9% on D360. Prevotella_1 established an absolute advantage in the rumen after 7 days of age. The co-occurrence network showed that the different microbial of the rumen presented a complex synergistic and cumbersome relationship. A phylogenetic tree was constructed, indicating that during the colonization process, may occur a phenomenon in which bacteria with close kinship are preferentially colonized. Overall, this study provides new insights into the colonization of bacterial communities in lambs that will benefit the development of management strategies to promote colonization of target communities to improve functional development.

Microorganisms play important roles in soil improvement. Therefore, clarifying the contribution of environmental factors in shaping the microbial community structure is beneficial to improve soil fertility in karst rocky desertification areas. Here, the bacterial community structures of eight rhizospheric soil samples collected from perennial fruit plantations were analysed using an Illumina HiSeq2500 platform. The diversity and abundance of bacteria in rocky desertification areas were significantly lower than those in non-rocky desertification areas, while the bacterial community structure was not significantly different between root surface and non-root surface soils in the same rhizospheric soil samples. Proteobacteria predominated in rocky desertification areas, while Actinobacteria predominated in non-rocky desertification areas. Correlation analysis revealed that water-soluble phosphorus content (r 2  = 0.8258), latitude (r 2  = 0.7556), altitude (r 2  = 0.7501), and the age of fruit trees (r 2  = 0.7321) were positively correlated with the bacterial community structure, while longitude, pH, and total phosphorus content did not significantly influence the soil bacterial community structure. As water-soluble phosphorus content is derived from insoluble phosphorus minerals, supplementing phosphorus-solubilising bacteria to soils in rocky desertification areas is a feasible strategy for accelerating the dissolution of insoluble phosphorus minerals and improving agricultural production and environment ecology.

Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.

As a toxic element, excessive amounts of fluoride in environment can be harmful because of its antimicrobial activity, however little is known about the relationship between fluoride and the bacterial community in groundwater systems. Here, we use samples from a typical fluorosis area to test the hypothesis that fluoride concentration is a fundamental structuring factor for bacterial communities in groundwater. Thirteen groundwater samples were collected; high-throughput 16S rRNA gene sequencing and statistical analysis were conducted to compare the bacterial community composition in individual wells. The results showed that Proteobacteria, with most relative abundance in groundwater, decreased along the groundwater fluoride concentration. Additionally, relative abundances of 12 families were also statistically correlated with fluoride concentration. The bacterial community was significantly explained by TOC (P = 0.045) and fluoride concentration (P = 0.007) of groundwater. This suggests that fluoride and TOC likely plays an important role in shaping the microbial community structure in these groundwater systems. Our research suggest that fluoride concentration should be taken into consideration in future when evaluating microbial response to environmental conditions in groundwater system, especially for fluoride rich groundwater.

Growing evidence highlights an association between an imbalance in the composition and abundance of bacteria in the breast tissue (referred as microbial dysbiosis) and breast cancer in women. However, studies on the breast tissue microbiome have not been conducted in non-Hispanic Black (NHB) women. We investigated normal and breast cancer tissue microbiota from NHB and non-Hispanic White (NHW) women to identify distinct microbial signatures by race, stage, or tumor subtype. Using 16S rRNA gene sequencing, we observed that phylum Proteobacteria was most abundant in normal (n = 8), normal adjacent to tumor (normal pairs, n = 11), and breast tumors from NHB and NHW women (n = 64), with fewer Firmicutes, Bacteroidetes, and Actinobacteria. Breast tissues from NHB women had a higher abundance of genus Ralstonia compared to NHW tumors, which could explain a portion of the breast cancer racial disparities. Analysis of tumor subtype revealed enrichment of family Streptococcaceae in TNBC. A higher abundance of genus Bosea (phylum Proteobacteria) increased with stage. This is the first study to identify racial differences in the breast tissue microbiota between NHB and NHW women. Further studies on the breast cancer microbiome are necessary to help us understand risk, underlying mechanisms, and identify potential microbial targets.

To investigate the interactions between bacterial species in relation to the biotic and abiotic environmental fluctuations, free-living (FL), nanoparticle-associated (NP), and microparticle-associated (MP) bacterial community compositions (BCCs) were analyzed. A total of 267 samples were collected from July to December 2016 in the dynamic and shallow southern coastal water of Korea. The variations in BCC mostly depended on planktonic size fraction. Network analysis revealed water depth-dependent co-occurrence patterns of coastal bacterial communities. Higher interspecies connectivity was observed within FL bacteria than NP/MP bacteria, suggesting that FL bacteria with a streamlined genome may need other bacterial metabolites for survival, while the NP/MP copiotrophs may have the self-supporting capacity to produce the vital nutrients. The analysis of topological roles of individual OTUs in the network revealed that several groups of metabolically versatile bacteria (the marine Roseobacters, Flavobacteriales, Desulfobacterales, and SAR406 clade) acted as module hubs in different water depth. In conclusion, interspecies interactions dominated in FL bacteria, compared to NP and MP bacteria; modular structures of bacterial communities and keystone species strongly depended on the water depth-derived environmental factors. Furthermore, the multifunctional, versatile FL bacteria could play pivotal roles in dynamic shallow coastal ecosystems.

Bacteria inhabiting the gut of insects provide many benefits to their hosts, such as aiding in food digestion, reproduction, and immunity, tissue homeostasis, adaptation to environment and resistance to pathogen and pesticides. The cowpea beetle, Callosobruchus maculatus, is a serious cosmopolitan pest of pulses. This beetle has lent itself as a guinea pig for several ecological studies. It harbors a consortium of bacterial communities in its gut, but the evidence for their role in its physiology is fragmentary. In this work, we hypothesized that gut microbiota mediates C. maculatus resistance to dichlorvos (DDVP or O,O-dimethyl O-2,2-dichlorovinylphosphate) and represent the target of Lippia adoensis (Gambian Tea Bush) essential oil (EO). Symbiotic and aposymbiotic beetles were exposed to artificial cowpea seeds earlier treated with DDVP or EO. Adult mortality and changes in gut bacterial community composition and abundance were examined at F 1 and F 5 generations. The susceptibility of experimental beetles to DDVP was significantly affected by their symbiotic status. The adult mortality decreased across generations in DDVP treatments, and remained significantly higher in aposymbiotic groups. In EO treatments, the mortality was consistent irrespective of symbiotic status and experimental generations. When compared to DDVP and the Control, EO treatments had significantly lower bacterial richness and diversity, as well as lower abundance of Proteobacteria, Firmicutes, and Bacteroidetes. These results support our hypothesis and describe the responses of gut microbial communities to pesticide treatments. This could be of interest for developing new management strategies of this pest.

Bowel obstruction (OB) causes local and systemic dysfunctions. Here we investigated whether obstruction leads to alterations in microbiota community composition and total abundance, and if so whether these changes contribute to dysfunctions in OB. Partial colon obstruction was maintained in rats for 7 days. The mid colon and its intraluminal feces - proximal to the obstruction - were studied. OB did not cause bacterial overgrowth or mucosa inflammation, but induced profound changes in fecal microbiota composition and diversity. At the phylum level, the 16S rRNA sequencing showed a significant decrease in the relative abundance of Firmicutes with corresponding increases in Proteobacteria and Bacteroidetes in OB compared with sham controls. Daily treatment using broad spectrum antibiotics dramatically reduced total bacterial abundance, but increased the relative presence of Proteobacteria. Antibiotics eliminated viable bacteria in the spleen and liver, but not in the mesentery lymph node in OB. Although antibiotic treatment decreased muscle contractility in sham rats, it had little effect on OB-associated suppression of muscle contractility or inflammatory changes in the muscle layer. In conclusion, obstruction leads to marked dysbiosis in the colon. Antibiotic eradication of microbiota had limited effects on obstruction-associated changes in inflammation, motility, or bacterial translocation.

Leprosy is a chronic infectious peripheral neuropathy that is caused by Mycobacterium leprae, and the skin is one of its preferred target sites. However, the effects of this infection on the skin microbiome remain largely unexplored. Here, we characterize and compare the lesional and non-lesional skin microbiomes of leprosy patients and healthy individuals through the deep sequencing of 16 S rRNA genes. Additionally, a subset of patients was monitored throughout the multi-drug therapy to investigate its effect on the leprous skin microbiome. Firmicutes-associated OTUs (primarily Staphylococcus) prevailed in healthy individuals. By contrast, Firmicutes was underrepresented and Proteobacteria was enriched in the patients' skin, although a single dominant taxon has not been observed at a finer taxonomic resolution. These differences can be explained by the significant decrease in Staphylococcus and Streptococcus as well as the enrichment in Brevundimonas. The overrepresentation of Micrococcus in patients is also remarkable. Genus-level compositional profiles revealed no significant intrapersonal difference between lesional and non-lesional sites. Treatment-associated changes indicated a loss of diversity and a shift in the community composition, with stronger impacts on the OTUs that are considered indigenous bacteria. Therefore, the molecular signatures associated with leprosy identified herein might be of importance for early diagnostics.

Arsenic contamination of drinking water affects more than 140 million people worldwide. While toxic to humans, inorganic forms of arsenic (arsenite and arsenate), can be used as energy sources for microbial respiration. AioX and its orthologues (ArxX and ArrX) represent the first members of a new sub-family of periplasmic-binding proteins that serve as the first component of a signal transduction system, that's role is to positively regulate expression of arsenic metabolism enzymes. As determined by X-ray crystallography for AioX, arsenite binding only requires subtle conformational changes in protein structure, providing insights into protein-ligand interactions. The binding pocket of all orthologues is conserved but this alone is not sufficient for oxyanion selectivity, with proteins selectively binding either arsenite or arsenate. Phylogenetic evidence, clearly demonstrates that the regulatory proteins evolved together early in prokaryotic evolution and had a separate origin from the metabolic enzymes whose expression they regulate.

Olfactory function is a key sense for human well-being and health, with olfactory dysfunction having been linked to serious diseases. As the microbiome is involved in normal olfactory epithelium development, we explored the relationship between olfactory function (odor threshold, discrimination, identification) and nasal microbiome in 67 healthy volunteers. Twenty-eight subjects were found to have normal olfactory function, 29 had a particularly good sense of smell ("good normosmics") and 10 were hyposmic. Microbial community composition differed significantly between the three olfactory groups. In particular, butyric acid-producing microorganisms were found to be associated with impaired olfactory function. We describe the first insights of the potential interplay between the olfactory epithelium microbial community and olfactory function, and suggest that the microbiome composition is able to mirror and potentially shape olfactory function by producing strong odor compounds.

Lakes are strongly influenced by wind-driven wave turbulence. The direct physical effects of turbulence on bacterioplankton community structure however, have not yet been addressed and remains poorly understood. To examine the stability of bacterioplankton communities under turbulent conditions, we simulated conditions in the field to evaluate the responses of the bacterioplankton community to physical forcing in Lake Taihu, using high-throughput sequencing and flow cytometry. A total of 4,520,231 high quality sequence reads and 74,842 OTUs were obtained in all samples with α-proteobacteria, γ-proteobacteria and Actinobacteria being the most dominant taxa. The diversity and structure of bacterioplankton communities varied during the experiment, but were highly similar based on the same time of sampling, suggesting that bacterioplankton communities are insensitive to wind wave turbulence in the lake. This stability could be associated with the traits associated with bacteria. In particular, turbulence favored the growth of bacterioplankton, which enhanced biogeochemical cycling of nutrients in the lake. This study provides a better understanding of bacterioplankton communities in lake ecosystems exposed to natural mixing/disturbances.

Walnuts (Juglans regia) have been associated with foodborne illness outbreaks in recent years. Thus, the purpose of this study was to investigate the distribution of bacteria on in-shell walnut surfaces from six representative provinces in China. The bacterial populations on walnut surfaces were investigated by high-throughput sequencing based on the bacterial 16 S rRNA hypervariable region V4. Twenty-eight samples were collected from fourteen regions in six provinces and harvested in different periods (the fresh in 2016 and the old in 2015). Proteobacteria was the most dominant phylum in all samples except for XJ1. In XJ1, and the most abundant phylum was Cyanobacteria, which also accounted for a large proportion of the abundance in YN1, YN11, XJ2 and SC11. In addition, Firmicutes and Actinobacteria were also the abundant phyla in the given samples. Some genera belonging to the opportunistic pathogens were detected, such as Pseudomonas, Acinetobacter, Burkholderia and Bacillus. The results revealed that the composition and abundance of bacterial consortiums on walnut surfaces varied among the geographical sites where they were harvested. Moreover, the storage time of samples also had impact on the abundance of bacteria. This study may provide a better understanding of the bacterial communities' diversity on in-shell walnut surfaces.

The Asian rice gall midge (ARGM) has emerged as a model gall forming pest of rice. The ARGM infestation of rice results in failure of panicle formation and economic loss. Understanding the molecular basis of ARGM-rice interactions is very crucial in order to control this devastating pest of rice. The current investigation was devised to identify bacterial communities present in the ARGM and in addition the bacterial diversity in the maggots during their interaction with susceptible or resistant rice varieties. Sequencing of 16S rRNA bacterial gene (V3-V4 region) revealed differences in the microflora of the ARGM maggots feeding on susceptible or resistant rice hosts. Results revealed that Wolbachia was the predominant bacterium in pupae and adults while Pseudomonas was predominant in maggots. Further, we observed that members of proteobacteria were predominant across all the samples. There was high species diversity in maggots isolated from susceptible rice and a high representation of unclassified bacteria in maggots isolated from resistant rice. This is the first study that reports variation of microbiome of the ARGM, based on host phenotype from which it was isolated, and results suggest that these variations could have an important role in host's susceptibility.

The aim of this study was to investigate the effects of dietary supplementation with two alternatives to antibiotics (Candida tropicalis and mulberry leaf flavonoids) on intestinal microbiota of preweaned calves challenged with Escherichia coli K99. Sixty Holstein calves were randomly assigned to 5 treatments: fed a basal diet (N-CON); fed a basal diet and challenged with E.coli K99 (P-CON); fed a basal diet supplemented with C.tropicalis (CT), mulberry leaf flavonoids (MLF), and the combination of the two additives (CM), respectively, and challenged with E.coli K99. The MLF and CM groups had significantly higher average daily grain and feed efficiency, and significantly lower fecal scores compared with the P-CON group after E. coli K99 challenge. The supplementation groups increased the relative abundance, at the phylum level, of Bacteroidetes and Proteobacteria, whereas at the genus level, they increased the relative abundance of Prevotella, Lactobacillus, and Enterococcus. Quantitative PCR revealed that the CT, MLF, and CM groups had significantly lower copy numbers of E.coli K99 compared with the P-CON group. The CT, MLF, and CM treatments reduce days of diarrhea, improve intestinal health, and beneficially manipulate the intestinal microbiota in preweaned calves.

Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.

Oral microorganisms are important determinants of health and disease. The source of the initial neonatal microbiome and the factors dictating initial human oral microbiota development are unknown. This study aimed to investigate this in placental, oral and gut microbiome profiles from 36 overweight or obese mother-baby dyads as determined by 16S rRNA sequencing. Expression of five antibiotic resistance genes of the β-lactamase class was analysed in the infant oral microbiota samples by QPCR. The neonatal oral microbiota was 65.35% of maternal oral, 3.09% of placental, 31.56% of unknown and 0% of maternal gut origin. Two distinct neonatal oral microbiota profiles were observed: one strongly resembling the maternal oral microbiota and one with less similarity. Maternal exposure to intrapartum antibiotics explained the segregation of the profiles. Families belonging to Proteobacteria were abundant after antibiotics exposure while the families Streptococcaceae, Gemellaceae and Lactobacillales dominated in unexposed neonates. 26% of exposed neonates expressed the Vim-1 antibiotic resistance gene. These findings indicate that maternal intrapartum antibiotic treatment is a key regulator of the initial neonatal oral microbiome.

In utero and upon delivery, neonates are exposed to a wide array of microorganisms from various sources, including maternal bacteria. Prior studies have proposed that the mode of feeding shapes the gut microbiota and, subsequently the child's health. However, the effect of the mode of feeding and its influence on the development of the neonatal oral microbiota in early infancy has not yet been reported. The aim of this study was to compare the oral microbiota of healthy infants that were exclusively breast-fed or formula-fed using 16S-rRNA gene sequencing. We demonstrated that the oral bacterial communities were dominated by the phylum Firmicutes, in both groups. There was a higher prevalence of the phylum Bacteroidetes in the mouths of formula-fed infants than in breast-fed infants (p = 0.01), but in contrast Actinobacteria were more prevalent in breast-fed babies; Proteobacteria was more prevalent in saliva of breast-fed babies than in formula-fed neonates (p = 0.04). We also found evidence suggesting that the oral microbiota composition changed over time, particularly Streptococcus species, which had an increasing trend between 4-8 weeks in both groups. This study findings confirmed that the mode of feeding influences the development of oral microbiota, and this may have implications for long-term human health.

Microbial communities reside in healthy tissues but are often disrupted during disease. Bacterial genomes and proteins are detected in brains from humans, nonhuman primates, rodents and other species in the absence of neurological disease. We investigated the composition and abundance of microbiota in frozen and fixed autopsied brain samples from patients with multiple sclerosis (MS) and age- and sex-matched nonMS patients as controls, using neuropathological, molecular and bioinformatics tools. 16s rRNA sequencing revealed Proteobacteria to be the dominant phylum with restricted diversity in cerebral white matter (WM) from MS compared to nonMS patients. Both clinical groups displayed 1,200-1,400 bacterial genomes/cm 3 and low bacterial rRNA:rDNA ratios in WM. RNAseq analyses showed a predominance of Proteobacteria in progressive MS patients' WM, associated with increased inflammatory gene expression, relative to a broader range of bacterial phyla in relapsing-remitting MS patients' WM. Although bacterial peptidoglycan (PGN) and RNA polymerase beta subunit immunoreactivities were observed in all patients, PGN immunodetection was correlated with demyelination and neuroinflammation in MS brains. Principal component analysis revealed that demyelination, PGN and inflammatory gene expression accounted for 86% of the observed variance. Thus, inflammatory demyelination is linked to an organ-specific dysbiosis in MS that could contribute to underlying disease mechanisms.

Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

The abundance and diversity of bacteria in two types of ponds were investigated by quantitative PCR and Illumina MiSeq sequencing. The results revealed that the abundance of bacterial 16S rRNA genes in D ponds (with grass carp fed sudan grass) was significantly lower than that in E ponds (with grass carp fed commercial feed). The microbial communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria in both E and D ponds, while the abundance of some genera was significantly different between the two types of ponds. Specifically, some potential pathogens such as Acinetobacter and Aeromonas were found to be significantly decreased, while some probiotics such as Comamonadaceae unclassified and Bacillales unclassified were significantly increased in D ponds. In addition, water quality of D ponds was better than that of E ponds. Temperature, dissolved oxygen and nutrients had significant influence on bacterial communities. The differences in bacterial community compositions between the two types of ponds could be partially explained by the different water conditions.

To enhance the treatment efficiency from an anaerobic digester, a novel six-compartment anaerobic/oxic baffled reactor (A/OBR) was employed. Two kinds of split-feeding A/OBRs R2 and R3, with influent fed in the 1 st , 3 rd and 5 th compartment of the reactor simultaneously at the respective ratios of 6:3:1 and 6:2:2, were compared with the regular-feeding reactor R1 when all influent was fed in the 1 st compartment (control). Three aspects, the COD removal, the hydraulic characteristics and the bacterial community, were systematically investigated, compared and evaluated. The results indicated that R2 and R3 had similar tolerance to loading shock, but the R2 had the highest COD removal of 91.6% with a final effluent of 345 mg/L. The mixing patterns in both split-feeding reactors were intermediate between plug-flow and completely-mixed, with dead spaces between 8.17% and 8.35% compared with a 31.9% dead space in R1. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis revealed that the split-feeding strategy provided a higher bacterial diversity and more stable bacterial community than that in the regular-feeding strategy. Further analysis indicated that Firmicutes, Bacteroidetes, and Proteobacteria were the dominant bacteria, among which Firmicutes and Bacteroidetes might be responsible for organic matter degradation and Proteobacteria for nitrification and denitrification.

The gut microbiota is involved in many aspects of host physiology but its role in body weight and glucose metabolism remains unclear. Here we studied the compositional changes of gut microbiota in diet-induced obesity mice that were conventionally raised or received microbiota transplantation. In conventional mice, the diversity of the faecal microbiota was weakly associated with 1(st) week weight gain but transferring the microbiota of mice with contrasting weight gain to germfree mice did not change obesity development or feed efficiency of recipients regardless whether the microbiota was taken before or after 10 weeks high fat (HF) feeding. Interestingly, HF-induced glucose intolerance was influenced by microbiota inoculation and improved glucose tolerance was associated with a low Firmicutes to Bacteroidetes ratio. Transplantation of Bacteroidetes rich microbiota compared to a control microbiota ameliorated glucose intolerance caused by HF feeding. Altogether, our results demonstrate that gut microbiota is involved in the regulation of glucose metabolism and the abundance of Bacteroidetes significantly modulates HF-induced glucose intolerance but has limited impact on obesity in mice. Our results suggest that gut microbiota is a part of complex aetiology of insulin resistance syndrome, individual microbiota composition may cause phenotypic variation associated with HF feeding in mice., Competing Interests: Nestec S.A. sponsored all the studies that were conducted by S.R., P.G. and A.B. C.J.C., M.M., F.B., D.M., J.S., C.L.L. and B.B. are employee of Nestec S.A. L.K. and R.B. were employee of Nestec S.A. during the time of studies.

Decomposition is a complex process involving the interaction of both biotic and abiotic factors. Microbes play a critical role in the process of carrion decomposition. In this study, we analysed bacterial communities from live rats and rat remains decomposed under natural conditions, or excluding sarcosaphagous insect interference, in China using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 1,394,842 high-quality sequences and 1,938 singleton operational taxonomic units were obtained. Bacterial communities showed notable variation in relative abundance and became more similar to each other across body sites during the decomposition process. As decomposition progressed, Proteobacteria (mostly Gammaproteobacteria) became the predominant phylum in both the buccal cavity and rectum, while Firmicutes and Bacteroidetes in the mouth and rectum, respectively, gradually decreased. In particular, the arrival and oviposition of sarcosaphagous insects had no obvious influence on bacterial taxa composition, but accelerated the loss of biomass. In contrast to the rectum, the microbial community structure in the buccal cavity of live rats differed considerably from that of rats immediately after death. Although this research indicates that bacterial communities can be used as a "microbial clock" for the estimation of post-mortem interval, further work is required to better understand this concept.

Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area.

The expansion of agriculture is shrinking pristine forest areas worldwide, jeopardizing the persistence of their wild inhabitants. The Udzungwa red colobus monkey (Procolobus gordonorum) is among the most threatened primate species in Africa. Primarily arboreal and highly sensitive to hunting and habitat destruction, they provide a critical model to understanding whether anthropogenic disturbance impacts gut microbiota diversity. We sampled seven social groups inhabiting two forests (disturbed vs. undisturbed) in the Udzungwa Mountains of Tanzania. While Ruminococcaceae and Lachnospiraceae dominated in all individuals, reflecting their role in extracting energy from folivorous diets, analysis of genus composition showed a marked diversification across habitats, with gut microbiota α-diversity significantly higher in the undisturbed forest. Functional analysis suggests that such variation may be associated with food plant diversity in natural versus human-modified habitats, requiring metabolic pathways to digest xenobiotics. Thus, the effects of changes in gut microbiota should not be ignored to conserve endangered populations.

Water-flooded oil reservoirs have specific ecological environments due to continual water injection and oil production and water recycling. Using 16S rRNA gene clone library analysis, the microbial communities present in injected waters and produced waters from four typical water-flooded oil reservoirs with different in situ temperatures of 25 °C, 40 °C, 55 °C and 70 °C were examined. The results obtained showed that the higher the in situ temperatures of the oil reservoirs is, the less the effects of microorganisms in the injected waters on microbial community compositions in the produced waters is. In addition, microbes inhabiting in the produced waters of the four water-flooded oil reservoirs were varied but all dominated by Proteobacteria. Moreover, most of the detected microbes were not identified as indigenous. The objective of this study was to expand the pictures of the microbial ecosystem of water-flooded oil reservoirs.