Research article Special Issues

Microbiome predictors of dysbiosis and VRE decolonization in patients with recurrent C. difficile infections in a multi-center retrospective study

  • Received: 01 November 2018 Accepted: 23 December 2018 Published: 17 January 2019
  • The gastrointestinal microbiome is intrinsically linked to the spread of antibiotic resistance. Antibiotic treatment puts patients at risk for colonization by opportunistic pathogens like vancomycin resistant Enterococcus and Clostridioides difficile by destroying the colonization resistance provided by the commensal microbiota. Once colonized, the host is at a much higher risk for infection by that pathogen. Furthermore, we know that microbiome community differences are associated with disease states, but we do not have a good understanding of how we can use these changes to classify different patient populations. To that end, we have performed a multicenter retrospective analysis on patients who received fecal microbiota transplants to treat recurrent Clostridioides difficile infection. We performed 16S rRNA gene sequencing on fecal samples collected as part of this study and used these data to develop a microbiome disruption index. Our microbiome disruption index is a simple index that is predictive across cohorts, indications, and batch effects. We are able to classify pre-fecal transplant vs post-fecal transplant samples in patients with recurrent C. difficile infection, and we are able to predict, using previously-published data from a cohort of patients receiving hematopoietic stem cell transplants, which patients would go on to develop bloodstream infections. Finally, we also identified patients in this cohort that were initially colonized with vancomycin resistant Enterococcus and that 92% (11/12) were decolonized after the transplant, but the microbiome disruption index was unable to predict such decolonization. We, however, were able to compare the relative abundance of different taxa between the two groups, and we found that increased abundance of Enterobacteriaceae predicts whether patients were colonized with vancomycin resistant Enterococcus. This work is an early step towards a better understanding of how microbiome predictors can be used to help improve patient care and patient outcomes.

    Citation: Marina Santiago, Lindsay Eysenbach, Jessica Allegretti, Olga Aroniadis, Lawrence J. Brandt, Monika Fischer, Ari Grinspan, Colleen Kelly, Casey Morrow, Martin Rodriguez, Majdi Osman, Zain Kassam, Mark B. Smith, Sonia Timberlake. Microbiome predictors of dysbiosis and VRE decolonization in patients with recurrent C. difficile infections in a multi-center retrospective study[J]. AIMS Microbiology, 2019, 5(1): 1-18. doi: 10.3934/microbiol.2019.1.1

    Related Papers:

    [1] Grégoire Allaire, Tuhin Ghosh, Muthusamy Vanninathan . Homogenization of stokes system using bloch waves. Networks and Heterogeneous Media, 2017, 12(4): 525-550. doi: 10.3934/nhm.2017022
    [2] Vivek Tewary . Combined effects of homogenization and singular perturbations: A bloch wave approach. Networks and Heterogeneous Media, 2021, 16(3): 427-458. doi: 10.3934/nhm.2021012
    [3] Carlos Conca, Luis Friz, Jaime H. Ortega . Direct integral decomposition for periodic function spaces and application to Bloch waves. Networks and Heterogeneous Media, 2008, 3(3): 555-566. doi: 10.3934/nhm.2008.3.555
    [4] Alexei Heintz, Andrey Piatnitski . Osmosis for non-electrolyte solvents in permeable periodic porous media. Networks and Heterogeneous Media, 2016, 11(3): 471-499. doi: 10.3934/nhm.2016005
    [5] Hiroshi Matano, Ken-Ichi Nakamura, Bendong Lou . Periodic traveling waves in a two-dimensional cylinder with saw-toothed boundary and their homogenization limit. Networks and Heterogeneous Media, 2006, 1(4): 537-568. doi: 10.3934/nhm.2006.1.537
    [6] Patrizia Donato, Florian Gaveau . Homogenization and correctors for the wave equation in non periodic perforated domains. Networks and Heterogeneous Media, 2008, 3(1): 97-124. doi: 10.3934/nhm.2008.3.97
    [7] Hakima Bessaih, Yalchin Efendiev, Florin Maris . Homogenization of the evolution Stokes equation in a perforated domain with a stochastic Fourier boundary condition. Networks and Heterogeneous Media, 2015, 10(2): 343-367. doi: 10.3934/nhm.2015.10.343
    [8] Patrick Henning . Convergence of MsFEM approximations for elliptic, non-periodic homogenization problems. Networks and Heterogeneous Media, 2012, 7(3): 503-524. doi: 10.3934/nhm.2012.7.503
    [9] Xavier Blanc, Claude Le Bris . Improving on computation of homogenized coefficients in the periodic and quasi-periodic settings. Networks and Heterogeneous Media, 2010, 5(1): 1-29. doi: 10.3934/nhm.2010.5.1
    [10] Grigor Nika, Adrian Muntean . Hypertemperature effects in heterogeneous media and thermal flux at small-length scales. Networks and Heterogeneous Media, 2023, 18(3): 1207-1225. doi: 10.3934/nhm.2023052
  • The gastrointestinal microbiome is intrinsically linked to the spread of antibiotic resistance. Antibiotic treatment puts patients at risk for colonization by opportunistic pathogens like vancomycin resistant Enterococcus and Clostridioides difficile by destroying the colonization resistance provided by the commensal microbiota. Once colonized, the host is at a much higher risk for infection by that pathogen. Furthermore, we know that microbiome community differences are associated with disease states, but we do not have a good understanding of how we can use these changes to classify different patient populations. To that end, we have performed a multicenter retrospective analysis on patients who received fecal microbiota transplants to treat recurrent Clostridioides difficile infection. We performed 16S rRNA gene sequencing on fecal samples collected as part of this study and used these data to develop a microbiome disruption index. Our microbiome disruption index is a simple index that is predictive across cohorts, indications, and batch effects. We are able to classify pre-fecal transplant vs post-fecal transplant samples in patients with recurrent C. difficile infection, and we are able to predict, using previously-published data from a cohort of patients receiving hematopoietic stem cell transplants, which patients would go on to develop bloodstream infections. Finally, we also identified patients in this cohort that were initially colonized with vancomycin resistant Enterococcus and that 92% (11/12) were decolonized after the transplant, but the microbiome disruption index was unable to predict such decolonization. We, however, were able to compare the relative abundance of different taxa between the two groups, and we found that increased abundance of Enterobacteriaceae predicts whether patients were colonized with vancomycin resistant Enterococcus. This work is an early step towards a better understanding of how microbiome predictors can be used to help improve patient care and patient outcomes.


    It is well known that the classical boundary conditions cannot describe certain peculiarities of physical, chemical, or other processes occurring within the domain. In order to overcome this situation, the concept of nonlocal conditions was introduced by Bicadze and Samarskiĭ [1]. These conditions are successfully employed to relate the changes happening at nonlocal positions or segments within the given domain to the values of the unknown function at end points or boundary of the domain. For a detailed account of nonlocal boundary value problems, for example, we refer the reader to the articles [2,3,4,5,6] and the references cited therein.

    Computational fluid dynamics (CFD) technique directly deals with the boundary data [7]. In case of fluid flow problems, the assumption of circular cross-section is not justifiable for curved structures. The idea of integral boundary conditions serves as an effective tool to describe the boundary data on arbitrary shaped structures. One can find application of integral boundary conditions in the study of thermal conduction, semiconductor, and hydrodynamic problems [8,9,10]. In fact, there are numerous applications of integral boundary conditions in different disciplines such as chemical engineering, thermoelasticity, underground water flow, population dynamics, etc. [11,12,13]. Also, integral boundary conditions facilitate to regularize ill-posed parabolic backward problems, for example, mathematical models for bacterial self-regularization [14]. Some recent results on boundary value problems with integral boundary conditions can be found in the articles [15,16,17,18,19] and the references cited therein.

    The non-uniformities in form of points or sub-segments on the heat sources can be relaxed by using the integro multi-point boundary conditions, which relate the sum of the values of the unknown function (e.g., temperature) at the nonlocal positions (points and sub-segments) and the value of the unknown function over the given domain. Such conditions also find their utility in the diffraction problems when scattering boundary consists of finitely many sub-strips (finitely many edge-scattering problems). For details and applications in engineering problems, for instance, see [20,21,22,23].

    The subject of fractional calculus has emerged as an important area of research in view of extensive applications of its tools in scientific and technical disciplines. Examples include neural networks [24,25], immune systems [26], chaotic synchronization [27,28], Quasi-synchronization [29,30], fractional diffusion [31,32,33], financial economics [34], ecology [35], etc. Inspired by the popularity of this branch of mathematical analysis, many researchers turned to it and contributed to its different aspects. In particular, fractional order boundary value problems received considerable attention. For some recent results on fractional differential equations with multi-point and integral boundary conditions, see [36,37]. More recently, in [38,39], the authors analyzed boundary value problems involving Riemann-Liouville and Caputo fractional derivatives respectively. A boundary value problem involving a nonlocal boundary condition characterized by a linear functional was studied in [40]. In a recent paper [41], the existence results for a dual anti-periodic boundary value problem involving nonlinear fractional integro-differential equations were obtained.

    On the other hand, fractional differential systems also received considerable attention as such systems appear in the mathematical models associated with physical and engineering processes [42,43,44,45,46]. For theoretical development of such systems, for instance, see the articles [47,48,49,50,51,52].

    Motivated by aforementioned applications of nonlocal integral boundary conditions and fractional differential systems, in this paper, we study a nonlinear mixed-order coupled fractional differential system equipped with a new set of nonlocal multi-point integral boundary conditions on an arbitrary domain given by

    $ {cDξa+x(t)=φ(t,x(t),y(t)),0<ξ1,t[a,b],cDζa+y(t)=ψ(t,x(t),y(t)),1<ζ2,t[a,b],px(a)+qy(b)=y0+x0ba(x(s)+y(s))ds,y(a)=0,y(b)=mi=1δix(σi)+λbτx(s)ds,a<σ1<σ2<<σm<τ<b,
    $
    (1.1)

    where $ ^c {D}^{\chi} $ is Caputo fractional derivative of order $ \chi\in\{\xi, \zeta\}, \varphi, \psi:[a, b]\times \mathbb{R}\times \mathbb{R}\rightarrow \mathbb{R} $ are given functions, $ \; p, q, \delta_i, x_0, y_0 \in \mathbb {R}, i = 1, 2, \ldots, m. $

    Here we emphasize that the novelty of the present work lies in the fact that we introduce a coupled system of fractional differential equations of different orders on an arbitrary domain equipped with coupled nonlocal multi-point integral boundary conditions. It is imperative to notice that much of the work related to the coupled systems of fractional differential equations deals with the fixed domain. Thus our results are more general and contribute significantly to the existing literature on the topic. Moreover, several new results appear as special cases of the work obtained in this paper.

    We organize the rest of the paper as follows. In Section 2, we present some basic concepts of fractional calculus and solve the linear version of the problem (1.1). Section 3 contains the main results. Examples illustrating the obtained results are presented in Section 4. Section 5 contains the details of a variant problem. The paper concludes with some interesting observations.

    Let us recall some definitions from fractional calculus related to our study [53].

    Definition 2.1. The Riemann–Liouville fractional integral of order $ \alpha\in\mathbb R $ ($ \alpha > 0 $) for a locally integrable real-valued function $ \varrho $ of order $ \alpha\in\mathbb R $, denoted by $ I_{a^+} ^\alpha \varrho $, is defined as

    $ I_{a^+} ^\alpha \varrho \left( t \right) = \left(\varrho*\frac{t^{\alpha-1}}{\Gamma(\alpha)}\right)(t) = {\rm{ }}\frac{1}{{\Gamma \left( \alpha \right)}}\int\limits_a^t {\left( {t - s} \right)^{\alpha - 1} \varrho\left( s \right)} ds, \, -\infty\leq a < t < b\leq+\infty, $

    where $ \Gamma $ denotes the Euler gamma function.

    Definition 2.2. The Riemann–Liouville fractional derivative $ D_{a^+} ^\alpha \varrho $ of order $ \alpha \in ]m-1, m], \, m\in \mathbb{N} $ is defined as

    $ D_{a^+} ^\alpha \varrho \left( t \right) = \frac{{d^m }}{{dt^m }}I_{a^+} ^{1 - \alpha } \varrho \left( t \right) = {\rm{}}\frac{1}{{\Gamma \left( m-\alpha \right)}}\frac{d^m}{dt^m}\int\limits_a^t {\left({t - s} \right)^{m-1-\alpha} \varrho \left( s \right)} ds, \, -\infty\leq a < t < b\leq+\infty, $

    while the Caputo fractional derivative $ {^c{D}_{a^+}^\alpha}u $ is defined as

    $ cDαa+ϱ(t)=Dαa+[ϱ(t)ϱ(a)ϱ(a)(ta)1!ϱ(m1)(a)(ta)m1(m1)!],
    $

    for $ \varrho, \varrho^{(m)} \in L^1[a, b]. $

    Remark 2.1. The Caputo fractional derivative $ {^c{D}_{a^+}^\alpha}\varrho $ is also defined as

    $ cDαϱ(t)=1Γ(mα)t0(ts)mα1ϱ(m)(s)ds.
    $

    In the following lemma, we obtain the integral solution of the linear variant of the problem (1.1).

    Lemma 2.1. Let $ \Phi, \Psi\in C([a, b], {\mathbb R}). $ Then the unique solution of the system

    $ {cDξa+x(t)=Φ(t),0<ξ1,t[a,b],cDζa+y(t)=Ψ(t),1<ζ2,t[a,b],px(a)+qy(b)=y0+x0ba(x(s)+y(s))ds,y(a)=0,y(b)=mi=1δix(σi)+λbτx(s)ds,a<σ1<σ2<<σm<τ<b,
    $
    (2.1)

    is given by a pair of integral equations

    $ x(t)=Iξa+Φ(t)+1Δ{y0+x0ba(bs)ξΓ(ξ+1)Φ(s)ds+ba(x0(bs)ζΓ(ζ+1)+ε1(bs)ζ2Γ(ζ1)q(bs)ξ1Γ(ξ))Ψ(s)dsε1mi=1δiσia(σis)ξ1Γ(ξ)Φ(s)dsε1λbτsa(su)ξ1Γ(ξ)Φ(u)duds},
    $
    (2.2)
    $ y(t)=Iζa+Ψ(t)+(ta)Δ{ε2y0+ε2x0ba(bs)ξΓ(ξ+1)Φ(s)ds+ba(ε2x0(bs)ζΓ(ζ+1)ε2q(bs)ξ1Γ(ξ)ε3(bs)ζ2Γ(ζ1))Ψ(s)ds+ε3mi=1δiσia(σis)ξ1Γ(ξ)Φ(s)ds+ε3λbτsa(su)ξ1Γ(ξ)Φ(u)duds},
    $
    (2.3)

    where

    $ ε1=q(ba)x0(ba)22,ε2=mi=1δi+λ(bτ),ε3=p(ba)x0,
    $
    (2.4)

    and it is assumed that

    $ Δ=ε3+ε2ε10.
    $
    (2.5)

    Proof. Applying the integral operators $ I_{a^+}^\xi $ and $ I_{a^+}^\zeta $ respectively on the first and second fractional differential equations in (2.1), we obtain

    $ x(t)=Iξa+Φ(t)+c1andy(t)=Iζa+Ψ(t)+c2+c3(ta),
    $
    (2.6)

    where $ c_i \in \mathbb{R}, {i = 1, 2, 3} $ are arbitrary constants. Using the condition $ y(a) = 0 $ in (2.6), we get $ c_2 = 0 $. Making use of the conditions $ px(a)+qy(b) = y_0 + x_0\int_{a}^{b}(x(s)+y(s))ds $ and $ y'(b) = \sum_{i = 1}^{m}\delta_ix(\sigma_i)+\lambda\int_{\tau}^{b}x(s)ds $ in (2.6) after inserting $ c_2 = 0 $ in it leads to the following system of equations in the unknown constants $ c_1 $ and $ c_3 $:

    $ (p(ba)x0)c1+(q(ba)x0(ba)22)c3=y0+x0ba(br)ξΓ(ξ+1)Φ(r)dr+x0ba(br)ζΓ(ζ+1)Ψ(r)drqIζa+Ψ(b),
    $
    (2.7)
    $ (mi=1δi+λ(bτ))c1c3=Iζ1a+Ψ(b)mi=1δiIξa+Φ(σi)λbτIξa+Φ(s)ds.
    $
    (2.8)

    Solving (2.7) and (2.8) for $ c_1 $ and $ c_3 $ and using the notation (2.5), we find that

    $ c1=1Δ{ε1(Iζ1a+Ψ(b)mi=1δiIξa+Φ(σi)λbτIξa+Φ(s)ds)+y0+x0ba(br)ξΓ(ξ+1)Φ(r)dr+x0ba(br)ζΓ(ζ+1)Ψ(r)drqIξa+Ψ(b)},c3=1Δ{ε2(y0+ba(br)ξΓ(ξ+1)Φ(r)dr+x0ba(br)ζΓ(ζ+1)Ψ(r)drqIξa+Ψ(b))ε3(Iζ1a+Ψ(b)mi=1δiIξa+Φ(σi)λbτIξa+Φ(s)ds)}.
    $

    Inserting the values of $ c_1, c_2, $ and $ c_3 $ in (2.6) leads to the solution (2.2) and (2.3). One can obtain the converse of the lemma by direct computation. This completes the proof.

    Let $ X = C([a, b], \mathbb{R}) $ be a Banach space endowed with the norm $ \Vert x\Vert = \sup\{\vert x(t)\vert, t \in[a, b]\}. $

    In view of Lemma 2.1, we define an operator $ T:X \times X \rightarrow X $ by:

    $ T(x(t),y(t)) = (T_1(x(t),y(t)),T_2(x(t),y(t))), $

    where $ (X \times X, \Vert (x, y)\Vert) $ is a Banach space equipped with norm $ \Vert(x, y)\Vert = \Vert x\Vert+\Vert y\Vert, x, y\in X, $

    $ T1(x,y)(t)=Iξa+φ(t,x(t),y(t))+1Δ(y0+x0ba(bs)ξΓ(ξ+1)φ(s,x(s),y(s))ds+baρ1(s)ψ(s,x(s),y(s))dsε1mi=1δiσia(σis)ξ1Γ(ξ)φ(s,x(s),y(s))dsε1λbτsa(su)ξ1Γ(ξ)φ(u,x(u),y(u))duds),T2(x,y)(t)=Iζa+ψ(t,x(t),y(t))+(ta)Δ(ε2y0+ε2x0ba(bs)ξΓ(ξ+1)φ(s,x(s),y(s))ds+baρ2(s)ψ(s,x(s),y(s))ds+ε3mi=1δiσia(σis)ξ1Γ(ξ)φ(s,x(s),y(s))ds+ε3λbτsa(su)ξ1Γ(ξ)φ(u,x(u),y(u))duds),
    $
    $ ρ1(s)=x0(bs)ζΓ(ζ+1)+ε1(bs)ζ2Γ(ζ1)q(bs)ξ1Γ(ξ),ρ2(s)=ε2x0(bs)ζΓ(ζ+1)ε2q(bs)ξ1Γ(ξ)ε3(bs)ζ2Γ(ζ1).
    $

    For computational convenience we put:

    $ L1=(ba)ξΓ(ξ+1)+1|Δ|(|x0|(ba)ξ+1Γ(ξ+2)+|ε1|mi=1|δi|(σia)ξΓ(ξ+1)+|ε1λ||(ba)ξ+1(τa)ξ+1|Γ(ξ+2)),M1=1|Δ|(|x0|(ba)ζ+1Γ(ζ+2)+|ε1|(ba)ζ1Γ(ζ)+|q|(ba)ξΓ(ξ+1)),L2=(ba)|Δ|(|ε2x0|(ba)ξ+1Γ(ξ+2)+|ε3|mi=1|δi|(σia)ξΓ(ξ+1)+|ε3λ||(ba)ξ+1(τa)ξ+1|Γ(ξ+2)),M2=(ba)ζΓ(ζ+1)+ba|Δ|(|ε2x0|(ba)ζ+1Γ(ζ+2)+|ε2q|(ba)ξΓ(ξ+1)+|ε3|(ba)ζ1Γ(ζ)).
    $
    (3.1)

    Our first existence result for the system (1.1) relies on Leray-Schauder alternative [54].

    Theorem 3.1. Assume that:

    $ (H_1) \; \varphi, \psi :[a, b] \times \mathbb{R} \times \mathbb{R} \rightarrow \mathbb{R} $ are continuous functions and there exist real constants $ k_i, \gamma_i \geq 0, \; (i = 1, 2) $ and $ k_0 > 0, \gamma_0 > 0 $ such that $ \forall x, y \in \mathbb{R}, $

    $ |φ(t,x,y)|k0+k1|x|+k2|y|,|ψ(t,x,y)|γ0+γ1|x|+γ2|y|.
    $

    Then there exists at least one solution for the system (1.1) on $ [a, b] $ if

    $ (L1+L2)k1+(M1+M2)γ1<1and(L1+L2)k2+(M1+M2)γ2<1,
    $
    (3.2)

    where $ L_i, M_i, i = 1, 2 $ are given by (3.1).

    Proof. Let us note that continuity of the functions $ \varphi $ and $ \psi $ implies that of the operator $ T: X \times X \rightarrow X \times X. $ Next, let $ \Omega \subset X \times X $ be bounded such that

    $ |φ(t,x(t),y(t))|K1,|ψ(t,x(t),y(t))|K2,(x,y)Ω,
    $

    for positive constants $ K_1 $ and $ K_2 $. Then for any $ (x, y)\in\Omega, $ we have

    $ |T1(x,y)(t)|Iξa+|φ(t,x(t),y(t))|+1|Δ|(|y0|+|x0|ba(bs)ξΓ(ξ+1)|φ(s,x(s),y(s))|ds+ba|ρ1(s)||ψ(s,x(s),y(s))|ds+|ε1|mi=1|δi|σia(σis)ξ1Γ(ξ)|φ(s,x(s),y(s))|ds+|ε1λ|bτsa(su)ξ1Γ(ξ)|φ(u,x(u),y(u))|duds)|y0||Δ|+{(ba)ξΓ(ξ+1)+1|Δ|(|x0|(ba)ξ+1Γ(ξ+2)+|ε1|mi=1|δi|(σia)ξΓ(ξ+1)+|ε1λ||(ba)ξ+1(τa)ξ+1|Γ(ξ+2))}K1+{1|Δ|(|x0|(ba)ζ+1Γ(ζ+2)+|ε1|(ba)ζ1Γ(ζ)+|q|(ba)ξΓ(ξ+1))}K2=|y0||Δ|+L1K1+M1K2,
    $
    (3.3)

    which implies that

    $ T1(x,y)|y0||Δ|+L1K1+M1K2.
    $

    In a similar manner, one can obtain that

    $ T2(x,y)|ε2y0|(ba)|Δ|+L2K1+M2K2.
    $

    In consequence, the operator $ T $ is uniformly bounded as

    $ T(x,y)|y0||Δ|+|ε2y0|(ba)|Δ|+(L1+L2)K1+(M1+M2)K2.
    $

    Now we show that T is equicontinuous. Let $ t_1, t_2\in[a, b] $ with $ t_1 < t_2. $ Then we have

    $ |T1(x(t2),y(t2))T1(x(t1),y(t1))|K1|1Γ(ξ)t2a(t2s)ξ1ds1Γ(ξ)t1a(t1s)ξ1ds|K1{1Γ(ξ)t1a[(t2s)ξ1(t1s)ξ1]ds+1Γ(ξ)t2t1(t2s)ξ1ds}K1Γ(ξ+1)[2(t2t1)ξ+|tξ2tξ1|].
    $
    (3.4)

    Analogously, we can obtain

    $ |T2(x(t2),y(t2))T2(x(t1),y(t1))|K2Γ(ζ+1)[2(t2t1)ζ+|tζ2tζ1|]+|t2t1||Δ|{|ε2x0|(ba)ξ+1Γ(ξ+2)K1+(|ε2x0|(ba)ζ+1Γ(ζ+2)+|ε2q|(ba)ξΓ(ξ+1)+|ε3|(ba)ζ1Γ(ζ))K2+|ε3|mi=1|δi|(σ1b)ξΓ(ξ+1)K1+|ε3λ||(ba)ξ+1(τa)ξ+1|Γ(ξ+2)K1}.
    $

    From the preceding inequalities, it follows that the operator $ T(x, y) $ is equicontinuous. Thus the operator $ T(x, y) $ is completely continuous.

    Finally, we consider the set $ \mathcal{P} = \lbrace (x, y) \in X \times X:(x, y) = \nu T(x, y), 0 \leq \nu\leq 1\rbrace $ and show that it is bounded.

    Let $ (x, y) \in \mathcal{P} $ with $ (x, y) = \nu T(x, y). $ For any $ t \in [a, b], $ we have $ x(t) = \nu T_1(x, y)(t), y(t) = \nu T_2(x, y)(t). $ Then by $ (H_1) $ we have

    $ |x(t)||y0||Δ|+L1(k0+k1|x|+k2|y|)+M1(γ0+γ1|x|+γ2|y|)=|y0||Δ|+L1k0+M1γ0+(L1k1+M1γ1)|x|+(L1k2+M1γ2)|y|,
    $

    and

    $ |y(t)||ε2y0|(ba)|Δ|+L2(k0+k1|x|+k2|y|)+M2(γ0+γ1|x|+γ2|y|)=|ε2y0|(ba)|Δ|+L2k0+M2γ0+(L2k1+M2γ1)|x|+(L2k2+M2γ2)|y|.
    $

    In consequence of the above inequalities, we deduce that

    $ x|y0||Δ|+L1k0+M1γ0+(L1k1+M1γ1)x+(L1k2+M1γ2)y,
    $

    and

    $ y|ε2y0|(ba)|Δ|+L2k0+M2γ0+(L2k1+M2γ1)x+(L2k2+M2γ2)y,
    $

    which imply that

    $ x+y|y0||Δ|+|ε2y0|(ba)|Δ|+(L1+L2)k0+(M1+M2)γ0+[(L1+L2)k1+(M1+M2)γ1]x+[(L1+L2)k2+(M1+M2)γ2]y.
    $

    Thus

    $ (x,y)1M0[|y0||Δ|+|ε2y0|(ba)|Δ|+(L1+L2)k0+(M1+M2)γ0],
    $

    where $ M_0 = \min \lbrace1-[(L_1+L_2)k_1+(M_1+M_2)\gamma_1], 1-[(L_1+L_2)k_2+(M_1+M_2)\gamma_2] \rbrace. $ Hence the set $ \mathcal{P} $ is bounded. As the hypothesis of Leray-Schauder alternative [54] is satisfied, we conclude that the operator $ T $ has at least one fixed point. Thus the problem (1.1) has at least one solution on $ [a, b] $.

    By using Banach's contraction mapping principle we prove in the next theorem the existence of a unique solution of the system (1.1).

    Theorem 3.2. Assume that:

    $ (H_2) \; \varphi, \psi:[a, b]\times\mathbb{R}\times\mathbb{R}\rightarrow\mathbb{R} $ are continuous functions and there exist positive constants $ l_1 $ and $ l_2 $ such that for all $ t\in[a, b] $ and $ x_i, y_i\in\mathbb{R}, \; i = 1, 2, $ we have

    $ |φ(t,x1,x2)φ(t,y1,y2)|l1(|x1y1|+|x2y2|),
    $
    $ |ψ(t,x1,x2)ψ(t,y1,y2)|l2(|x1y1|+|x2y2|).
    $

    If

    $ (L1+L2)l1+(M1+M2)l2<1,
    $
    (3.5)

    where $ L_i, M_i, i = 1, 2 $ are given by (3.1) then the system (1.1) has a unique solution on $ [a, b] $.

    Proof. Define $ \sup_{t\in[a, b]}\varphi(t, 0, 0) = N_1 < \infty, $ $ \sup_{t\in[a, b]}\psi(t, 0, 0) = N_2 < \infty $ and $ r > 0 $ such that

    $ r>(|y0|/|Δ|)(1+(ba)|ε2|)+(L1+L2)N1+(M1+M2)N21(L1+L2)l1(M1+M2)l2.
    $

    Let us first show that $ T B_r \subset B_r, $ where $ B_r = \lbrace(x, y)\in X \times X : \Vert (x, y) \Vert \leq r\rbrace. $ By the assumption $ (H_2), $ for $ (x, y) \in B_r, \; t \in [a, b], $ we have

    $ |φ(t,x(t),y(t))||φ(t,x(t),y(t))φ(t,0,0)|+|φ(t,0,0)|l1(|x(t)|+|y(t)|)+N1l1(x+y)+N1l1r+N1.
    $
    (3.6)

    Similarly, we can get

    $ |ψ(t,x(t),y(t))|l2(x+y)+N2l2r+N2.
    $
    (3.7)

    Using (3.6) and (3.7), we obtain

    $ |T1(x,y)(t)|Iξa+|φ(t,x(t),y(t))|+1|Δ|(|y0|+|x0|ba(bs)ξΓ(ξ+1)|φ(s,x(s),y(s))|ds+ba|ρ1(s)||ψ(s,x(s),y(s))|ds+|ε1|mi=1|δi|σia(σis)ξ1Γ(ξ)|φ(s,x(s),y(s))|ds+|ε1λ|bτsa(su)ξ1Γ(ξ)|φ(u,x(u),y(u))|duds)|y0||Δ|+{(ba)ξΓ(ξ+1)+1|Δ|(|x0|(ba)ξ+1Γ(ξ+2)+|ε1|mi=1|δi|(σia)ξΓ(ξ+1)+|ε1λ||(ba)ξ+1(τa)ξ+1|Γ(ξ+2))}(l1r+N1)+{1|Δ|(|x0|(ba)ζ+1Γ(ζ+2)+|ε1|(ba)ζ1Γ(ζ)+|q|(ba)ξΓ(ξ+1))}(l2r+N2)=|y0||Δ|+L1(l1r+N1)+M1(l2r+N2)=|y0||Δ|+(L1l1+M1l2)r+L1N1+M1N2.
    $
    (3.8)

    Taking the norm of (3.8) for $ t\in[a, b], $ we get

    $ T1(x,y)|y0||Δ|+(L1l1+M1l2)r+L1N1+M1N2.
    $

    Likewise, we can find that

    $ T2(x,y)|ε2y0|(ba)|Δ|+(L2l1+M2l2)r+L2N1+M2N2.
    $

    Consequently,

    $ T(x,y)|y0||Δ|+|ε2y0|(ba)|Δ|+[(L1+L2)l1+(M1+M2)l2]r+(L1+L2)N1+(M1+M2)N2r.
    $

    Now, for $ (x_1, y_1), (x_2, y_2) \in X \times X $ and for any $ t \in [a, b], $ we get

    $ |T1(x2,y2)(t)T1(x1,y1)(t)|{(ba)ξΓ(ξ+1)+1|Δ|(|x0|(ba)ξ+1Γ(ξ+2)+|ε1|mi=1|δi|(σia)ξΓ(ξ+1)+|ε1λ||(ba)ξ+1(τa)ξ+1|Γ(ξ+2))}l1(x2x1+y2y1)+{1|Δ|(|x0|(ba)ζ+1Γ(ζ+2)+|ε1|(ba)ζ1Γ(ζ)+|q|(ba)ξΓ(ξ+1))}l2(x2x1+y2y1)=(L1l1+M1l2)(x2x1+y2y1),
    $

    which implies that

    $ T1(x2,y2)T1(x1,y1)(L1l1+M1l2)(x2x1+y2y1).
    $
    (3.9)

    Similarly, we find that

    $ T2(x2,y2)T2(x1,y1)(L2l1+M2l2)(x2x1+y2y1).
    $
    (3.10)

    It follows from (3.9) and (3.10) that

    $ T(x2,y2)T(x1,y1)[(L1+L2)l1+(M1+M2)l2](x2x1+y2y1).
    $

    From the above inequality, we deduce that T is a contraction. Hence it follows by Banach's fixed point theorem that there exists a unique fixed point for the operator T, which corresponds to a unique solution of problem (1.1) on $ [a, b] $. This completes the proof.

    Consider the following mixed-type coupled fractional differential system

    $ {D34a+x(t)=φ(t,x(t),y(t)),t[1,2],D74a+y(t)=ψ(t,x(t),y(t)),t[1,2]15x(1)+110y(2)=1100021(x(s)+y(s))ds,y(1)=0,y(2)=2i=1δix(σi)+110274x(s)ds,
    $
    (3.11)

    where $ \xi = 3/4, \zeta = 7/4, p = 1/5, q = 1/10, x_0 = 1/1000, y_0 = 0, \delta_1 = 1/10, \delta_2 = 1/100, \sigma_1 = 5/4, \sigma_2 = 3/2, \tau = 7/4, \lambda = 1/10. $ With the given data, it is found that $ L_1\simeq 3.5495\times 10^{-2}, L_2\simeq 6.5531\times 10^{-2}, M_1\simeq 1.0229, M_2\simeq 0.90742. $

    (1) In order to illustrate Theorem 3.1, we take

    $ φ(t,x,y)=e2t+18xcosy+et3ysiny,ψ(t,x,y)=tt2+3+et3πxtan1y+148+t2y.
    $
    (3.12)

    It is easy to check that the condition $ (H_1) $ is satisfied with $ k_0 = 1/e^2, k_1 = 1/8, k_2 = 1/(3e), \gamma_0 = 2 \sqrt{7}, \gamma_1 = 1/(6e), \gamma_2 = 1/7. $ Furthermore, $ (L_1 + L_2)k_1 + (M_1 + M_2)\gamma_1\simeq 0.13098 < 1, $ and $ (L_1 + L_2)k_2 + (M_1 + M_2) \gamma_2 \simeq0.28815 < 1. $ Clearly the hypotheses of Theorem 3.1 are satisfied and hence the conclusion of Theorem 3.1 applies to problem (3.11) with $ \varphi $ and $ \psi $ given by (3.12).

    (2) In order to illustrate Theorem 3.2, we take

    $ φ(t,x,y)=et3+t2cosx+cost,ψ(t,x,y)=15+t4(sinx+|y|)+et,
    $
    (3.13)

    which clearly satisfy the condition $ (H_2) $ with $ l_1 = 1/(2e) $ and $ l_2 = 1/6. $ Moreover $ (L_1 +L_2)l_1 + (M_1 + M_2)l_2\simeq 0.3403 < 1. $ Thus the hypothesis of Theorem $ 3.2 $ holds true and consequently there exists a unique solution of the problem (3.11) with $ \varphi $ and $ \psi $ given by (3.13) on $ [1, 2]. $

    In this section, we consider a variant of the problem (1.1) in which the nonlinearities $ \varphi $ and $ \psi $ do not depend on $ x $ and $ y $ respectively. In precise terms, we consider the following problem:

    $ {cDξa+x(t)=¯φ(t,y(t)),0<ξ1,t[a,b],cDζa+y(t)=¯ψ(t,x(t)),1<ζ2,t[a,b],px(a)+qy(b)=y0+x0ba(x(s)+y(s))ds,y(a)=0,y(b)=mi=1δix(σi)+λbτx(s)ds,a<σ1<σ2<<σm<τ<<b,
    $
    (4.1)

    where $ \varphi, \psi:[a, b]\times \mathbb{R}\rightarrow \mathbb{R} $ are given functions. Now we present the existence and uniqueness results for the problem (4.1). We do not provide the proofs as they are similar to the ones for the problem (1.1).

    Theorem 4.1. Assume that $ \overline{ \varphi }, \overline { \psi } :[a, b] \times \mathbb{R} \rightarrow \mathbb{R} $ are continuous functions and there exist real constants $ \overline{k}_i, \overline{\gamma}_i \geq 0, \; (i = 0, 1) $ and $ \overline{k}_0 > 0, \overline{\gamma}_0 > 0 $ such that, $ \forall x, y \in \mathbb{R}, $

    $ |¯φ(t,y)|¯k0+¯k1|y|,|¯ψ(t,x)|¯γ0+¯γ1|x|.
    $

    Then the system (4.1) has at least one solution on $ [a, b] $ provided that $ (M_1+ M_2) \overline{\gamma}_1 < 1 $ and $ (L_1+ L_2)\overline{k}_1 < 1, $ where $ L_1, M_1 $ and $ L_2, M_2 $ are given by (3.1).

    Theorem 4.2. Let $ \overline{\varphi}, \overline{\psi}: [a, b] \times \mathbb{R} \rightarrow \mathbb{R} $ be continuous functions and there exist positive constants $ \overline{l}_1 $ and $ \overline{l}_2 $ such that, for all $ t\in[a, b] $ and $ x_i, y_i\in\mathbb{R}, \; i = 1, 2, $

    $ |¯φ(t,x1)¯φ(t,y1)|¯l1|x1y1|,|¯ψ(t,x1)¯ψ(t,y1)|¯l2|x1y1|.
    $

    If $ (L_1+L_2)\overline{l}_1+(M_1+M_2)\overline{l}_2 < 1, $ where $ L_1, M_1 $ and $ L_2, M_2 $ are given by (3.1) then the system (4.1) has a unique solution on $ [a, b] $.

    We studied the solvability of a coupled system of nonlinear fractional differential equations of different orders supplemented with a new set of nonlocal multi-point integral boundary conditions on an arbitrary domain by applying the tools of modern functional analysis. We also presented the existence results for a variant of the given problem containing the nonlinearities depending on the cross-variables (unknown functions). Our results are new not only in the given configuration but also yield some new results by specializing the parameters involved in the problems at hand. For example, by taking $ \delta_i = 0, i = 1, 2, \ldots, m $ in the obtained results, we obtain the ones associated with the coupled systems of fractional differential equations in (1.1) and (4.1) subject to the boundary conditions:

    $ px(a)+qy(b)=y0+x0ba(x(s)+y(s))ds,y(a)=0,y(b)=λbτx(s)ds.
    $

    For $ \lambda = 0 $, our results correspond to the boundary conditions of the form:

    $ px(a)+qy(b)=y0+x0ba(x(s)+y(s))ds,y(a)=0,y(b)=mi=1δix(σi).
    $
    (5.1)

    Furthermore, the methods employed in this paper can be used to solve the systems involving fractional integro-differential equations and multi-term fractional differential equations complemented with the boundary conditions considered in the problem (1.1).

    All authors declare no conflicts of interest in this paper.

    This project was funded by the Deanship of Scientific Research (DSR), King Abdulaziz University, Jeddah, Saudi Arabia under grant no. (KEP-PhD-41-130-41). The authors, therefore, acknowledge with thanks DSR technical and financial support. The authors also thank the reviewers for their useful suggestions on our work.


    Acknowledgments



    The microbiome disruption index was developed by OpenBiome with the assistance of Finch Therapeutics and the support of CDC (contract numbers 200-2016-91946 and 200-2016-91948).

    Conflict of interest



    MS, ZK, ST, and MBS are employees of Finch Therapeutics Group Inc. JRA consults for and had research support from Finch Therapeutics Group. AG is a consultant for Merck. The authors declare no conflicts of interest in this paper.

    [1] Antibiotic Resistance Threats in the United States, 2013. US Department of Health and Human Services, Centers for Disease Control and Prevention, 2013.
    [2] Knight GM, Costelloe C, Deeny SR, et al. (2018) Quantifying where human acquisition of antibiotic resistance occurs: a mathematical modelling study. BMC Med 16: 137. doi: 10.1186/s12916-018-1121-8
    [3] Sassone-Corsi M, Raffatellu M (2015) No vacancy: how beneficial microbes cooperate with immunity to provide colonization resistance to pathogens. J Immunol 194: 4081–4087. doi: 10.4049/jimmunol.1403169
    [4] Olsan EE, Byndloss MX, Faber F, et al. (2017) Colonization resistance: the deconvolution of a complex trait. J Biol Chem 292: 8577–8581. doi: 10.1074/jbc.R116.752295
    [5] McKenney ES, Kendall MM (2016) Microbiota and pathogen 'pas de deux': setting up and breaking down barriers to intestinal infection. Pathog Dis 74: ftw051. doi: 10.1093/femspd/ftw051
    [6] Sassone-Corsi M, Nuccio S, Liu H, et al. (2016) Microcins mediate competition among Enterobacteriaceae in the inflamed gut. Nature 540: 280–283. doi: 10.1038/nature20557
    [7] Brandl K, Plitas G, Mihu C, et al. (2008) Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits. Nature 455: 804–807. doi: 10.1038/nature07250
    [8] Theriot CM, Young VB (2015) Interactions between the gastrointestinal microbiome and Clostridium difficile. Annu Rev Microbiol 69: 445–461. doi: 10.1146/annurev-micro-091014-104115
    [9] Freedman A (2014) Use of stool transplant to clear fecal colonization with carbapenem-resistant Enterobacteraciae (CRE): proof of concept. IDWeek.
    [10] Singh R, Nood E, Nieuwdorp, et al. (2014) Donor feces infusion for eradication of Extended Spectrum beta-Lactamase producing Escherichia coli in a patient with end stage renal disease. Clin Microbiol Infec 20: O977–O978. doi: 10.1111/1469-0691.12683
    [11] Stripling J, Kumar R, Baddley JW, et al. (2015) Loss of vancomycin-resistant Enterococcus fecal dominance in an organ transplant patient with Clostridium difficile colitis after fecal microbiota transplant. Open Forum Infect Dis 2: 1–4.
    [12] Crun-Cianfione N, Sullivan E, Gonzalo B (2015) Fecal microbiota transplantation and successful resolution of multidrug-resistant-organism colonization. J Clin Microbiol 53: 1986–1989. doi: 10.1128/JCM.00820-15
    [13] Jang M, An J, Jung S, et al. (2014) Refractory Clostridium difficile infection cured with fecal microbiota transplantation in vancomycin-resistant Enterococcus colonized patient. Intest Res 13: 80–84.
    [14] Lombardo M (2015) Vancomycin-resistant enterococcal (VRE) titers diminish among patients with recurrent Clostridium difficile infection after administration of SER-109, a novel microbiome agent. IDWeek.
    [15] Biliński J, Grzesiowski P, Muszynski J, et al. (2016) Fecal microbiota transplantation inhibits multidrug-resistant gut pathogens: preliminary report performed in an immunocompromised host. Arch Immunol Ther Ex 64: 255–258. doi: 10.1007/s00005-016-0387-9
    [16] Lagier J, Million M, Fournier P, et al. (2015) Faecal microbiota transplantation for stool decolonization of OXA-48 carbapenemase-producing Klebsiella pneumoniae. J Hosp Infect 90: 173–174. doi: 10.1016/j.jhin.2015.02.013
    [17] Wei Y, Gong J, Zhu W, et al. (2015) Fecal microbiota transplantation restores dysbiosis in patients with methicillin resistant Staphylococcus aureus enterocolitis. BMC Infect Dis 15: 265. doi: 10.1186/s12879-015-0973-1
    [18] Eysenbach L, Allegretti JR, Aroniadis O, et al. (2016) Clearance of vancomycin-resistant Enterococcus colonization with fecal microbiota transplantation among patients with recurrent Clostridium difficile infection. IDWeek.
    [19] Dubberke ER, Mullane KM, Gerding DN, et al. (2016) Clearance of vancomycin-resistant Enterococcus concomitant with administration of a microbiota-based drug targeted at recurrent Clostridium difficile infection. Open Forum Infect Dis 3: ofw133. doi: 10.1093/ofid/ofw133
    [20] Jouhten H, Mattila E, Arkkila P, et al. (2016) Reduction of antibiotic resistance genes in intestinal microbiota of patients with recurrent Clostridium difficile infection after fecal microbiota transplantation. Clin Infect Dis 63: 710–711. doi: 10.1093/cid/ciw390
    [21] Millan B, Park H, Hotte N, et al. (2016) Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile infection. Clin Infect Dis 62: 1479–1486. doi: 10.1093/cid/ciw185
    [22] García-Fernández S, Morosini M, Cobo M, et al. (2016) Gut eradication of VIM-1 producing ST9 Klebsiella oxytoca after fecal microbiota transplantation for diarrhea caused by a Clostridium difficile hypervirulent R027 strain. Diagn Micr Infec Dis 86: 470–471. doi: 10.1016/j.diagmicrobio.2016.09.004
    [23] Sohn KM, Cheon S, Kim YS (2016) Can fecal microbiota transplantation (FMT) eradicate fecal colonization with vancomycin-resistant Enterococci (VRE)? Infect Cont Hosp Ep 37: 1519–1521.
    [24] Davido B, Batista R, Michelon H, et al. (2017) Is faecal microbiota transplantation an option to eradicate highly drug-resistant enteric bacteria carriage? J Hosp Infect 95: 433–437. doi: 10.1016/j.jhin.2017.02.001
    [25] Ponte A, Pinho R, Mota M (2017) Fecal microbiota transplantation: is there a role in the eradication of carbapenem-resistant Klebsiella pneumoniae intestinal carriage? Rev Esp Enferm Dig 109: 392.
    [26] Bilinski J, Grzesiowski P, Sorensen N, et al. (2017) Fecal microbiota transplantation in patients with blood disorders inhibits gut colonization with antibiotic-resistant bacteria: results of a prospective, single-center study. Clin Infect Dis 65: 364–370. doi: 10.1093/cid/cix252
    [27] Dias C, Pipa S, Duarte-Ribeiro F, et al. (2018) Fecal microbiota transplantation as a potential way to eradicate multiresistant microorganisms. IDCases 13: e00432. doi: 10.1016/j.idcr.2018.e00432
    [28] Safdar N, Sengupta S, Musuuza JS, et al. (2017) Status of the prevention of multidrug-resistant organisms in international settings: a survey of the society for healthcare epidemiology of america research network. Infect Cont Hosp Ep 38: 53–60. doi: 10.1017/ice.2016.242
    [29] Kelly CR, Khoruts A, Staley C, et al. (2016) Effect of fecal microbiota transplantation on recurrence in multiply recurrent Clostridium difficile infection: a randomized trial. Ann Intern Med 165: 609–616. doi: 10.7326/M16-0271
    [30] Kozich JJ, Westcott SL, Baxter NT, et al. (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microb 79: 5112–5120. doi: 10.1128/AEM.01043-13
    [31] Caporaso JG, Kucznyski J, Stombaugh J, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335–336. doi: 10.1038/nmeth.f.303
    [32] Taur Y, Xavier J, Lipuma L, et al. (2012) Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis 5: 905–914.
    [33] Moayyedi P, Yuan Y, Baharith H, et al. (2017) Faecal microbiota transplantation for Clostridium difficile-associated diarrhoea: a systematic review of randomised controlled trials. Med J Aust 207: 166–172. doi: 10.5694/mja17.00295
    [34] Burns LJ, Dubois N, Smith MB, et al. (2015) 499 donor recruitment and eligibility for fecal microbiota transplantation: results from an international public stool bank. Gastroenterology 48: 96–97.
    [35] Halpin AL, de Man TJB, Kraft CS, et al. (2016) Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention. Am J Infect Control 44: 830–836. doi: 10.1016/j.ajic.2016.01.003
    [36] Staley C, Kaiser T, Vaughn BP, et al. (2018) Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation. Microbiome 6: 166. doi: 10.1186/s40168-018-0549-6
    [37] Chang JY, Antonopoulos DA, Kaira A, et al. (2008) Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. J Infect Dis 197: 435–438. doi: 10.1086/525047
    [38] Fuentes S, van Nood E, Tims S, et al. (2014) Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection. ISME J 8: 1621–1633. doi: 10.1038/ismej.2014.13
    [39] Ubeda C, Taur Y, Jenq R, et al. (2010) Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest 120: 4332–4341. doi: 10.1172/JCI43918
    [40] Lebreton F, Willems RJL, Gilmore MS (2014) Enterococcus Diversity, Origins in Nature, and Gut Colonization, In: Enterococci: From Commensals to Leading Causes of Drug Resistant Infection, 4 Eds., Boston: Massachusetts Eye and Ear Infirmary.
    [41] Patel R, Piper KE, Rouse MS, et al. (1998) Determination of 16S rRNA sequences of Enterococci and application to species identification of nonmotile Enterococcus gallinarum isolates. J Clin Microbiol 36: 3399–3407.
    [42] Huttenhower C, Gevers D, Knight R, et al. (2012) Structure, function and diversity of the healthy human microbiome. Nature 486: 207–214. doi: 10.1038/nature11234
    [43] Kotlowski R, Bernstein CN, Sepehri S, et al. (2007) High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease. Gut 56: 669–675. doi: 10.1136/gut.2006.099796
    [44] Buffie CG, Jarchum I, Equinda M, et al. (2012) Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun 80: 62–73. doi: 10.1128/IAI.05496-11
    [45] Desai MS, Seekatz AM, Koropatkin NM, et al. (2016) A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167: 1339–1353. doi: 10.1016/j.cell.2016.10.043
    [46] Wu W, Sun M, Chen F, et al. (2016) Microbiota metabolite short-chain fatty acid acetate promotes intestinal IgA response to microbiota which is mediated by GPR43. Mucosal Immunol 10: 946–956.
    [47] Goverse G, Molenaar R, Maci L, et al. (2017) Diet-derived short chain fatty acids stimulate intestinal epithelial cells to induce mucosal tolerogenic dendritic cells. J Immunol 198: 2172–2181. doi: 10.4049/jimmunol.1600165
    [48] Faber F, Bäumler AJ (2014) The impact of intestinal inflammation on the nutritional environment of the gut microbiota. Immunol Lett 162: 48–53. doi: 10.1016/j.imlet.2014.04.014
    [49] Lopez CA, Winter SE, Rivera-Chavez F, et al. (2012) Phage-mediated acquisition of a type III secreted effector protein boosts growth of Salmonella by nitrate respiration. Mbio 3: e00143-12.
    [50] Winter SE, Winter MG, Xavier MN, et al. (2013) Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science 339: 708–711.
    [51] Thiennimitr P, Winter SE, Winter MG, et al. (2011) Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. P Natl Acad Sci USA 108: 17480–17485. doi: 10.1073/pnas.1107857108
    [52] Fujitani S, George WL, Morgan MA, et al. (2011) Implications for vancomycin-resistant Enterococcus colonization associated with Clostridium difficile infections. Am J Infect Control 39: 188–193. doi: 10.1016/j.ajic.2010.10.024
    [53] Sangster W, Hegarty JP, Schieffer KM, et al. (2016) Bacterial and fungal microbiota changes distinguish C. difficile infection from other forms of diarrhea: results of a prospective inpatient study. Front Microbiol 7: 789.
    [54] Horvat S, Mahnic A, Breskvar M, et al. (2017) Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure. Sci Rep 7: 16448. doi: 10.1038/s41598-017-15434-1
    [55] Papa E, Docktor M, Smillie C, et al. (2012) Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS One 7: e39242. doi: 10.1371/journal.pone.0039242
  • This article has been cited by:

    1. Shu Gu, Jinping Zhuge, Periodic homogenization of Green’s functions for Stokes systems, 2019, 58, 0944-2669, 10.1007/s00526-019-1553-9
    2. Vivek Tewary, Combined effects of homogenization and singular perturbations: A bloch wave approach, 2021, 16, 1556-181X, 427, 10.3934/nhm.2021012
    3. Kirill Cherednichenko, Serena D’Onofrio, Operator-norm homogenisation estimates for the system of Maxwell equations on periodic singular structures, 2022, 61, 0944-2669, 10.1007/s00526-021-02139-7
    4. T. Muthukumar, K. Sankar, Homogenization of the Stokes System in a Domain with an Oscillating Boundary, 2022, 20, 1540-3459, 1361, 10.1137/22M1474345
  • Reader Comments
  • © 2019 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
通讯作者: 陈斌, bchen63@163.com
  • 1. 

    沈阳化工大学材料科学与工程学院 沈阳 110142

  1. 本站搜索
  2. 百度学术搜索
  3. 万方数据库搜索
  4. CNKI搜索

Metrics

Article views(6396) PDF downloads(907) Cited by(10)

/

DownLoad:  Full-Size Img  PowerPoint
Return
Return

Catalog